KR20130082495A - Nucleic acid detection and quantification by post-hybridization labeling and universal encoding - Google Patents

Abstract

The present invention, among other things, provides methods and compositions for detection and quantification of target nucleic acids via post-hybrid labeling. In some embodiments, the present invention provides a method for detecting the presence and / or abundance of target nucleic acids in a sample, wherein (a) each binds to a capture sequence and a universal adapter that binds to the target nucleic acid. Contacting the sample with a plurality of nucleic acid probes consisting of contiguous adapter sequences; (b) culturing the plurality of probes and the sample under conditions in which one or more universal adapters are present and both individual target nucleic acids and individual universal adapters can be bound to the same individual nucleic acid probe; (c) conducting the reaction such that individual universal adapters are combined with individual target nucleic acids, and hybridizing with the same individual nucleic acid probes; (d) detecting the presence of one or more universal adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of target nucleic acids in the sample. Typically, universal adapters are labeled with detectable substances or other detectable trigger labeling groups. In some embodiments, a plurality of nucleic acid probes suitable for the present invention are attached to a substrate or a subject (eg, microarray, or particle).

Description

Nucleic acid detection and quantification by post hybrid hybridization and general coding {NUCLEIC ACID DETECTION AND QUANTIFICATION BY POST-HYBRIDIZATION LABELING AND UNIVERSAL ENCODING}

This application claims priority to US Provisional Patent Application No. 61 / 352,018, filed Jul. 19, 2010, filed July 19, 2010, and Application No. 61 / 387,958, filed Sep. 29, 2010, which are full Is incorporated herein by reference.

Multiple detection of biomolecules is important for clinical diagnosis, discovery, and basic science. Multiple detection requires coding the substrates to be linked with specific biomolecule targets and associating the detectable signal with the biomolecule target for which quantification is required. For multiplex analysis, targets are typically captured and quantified using planar or particle-based functionalized substrates. In particle-based multiplex analysis, each particle is functionalized with a probe that captures a specific target and is encoded to be identified during the analysis. In order to quantify the target content trapped in the particles, suitable labeling schemes are typically used to generate measurable signals associated with the target. A molecular class that is particularly difficult to quantify due to the limitations of existing labeling methods is microRNA (miRNA).

miRNAs are short non-coding RNAs that mediate protein translation and are known to be dysregulated in diseases including diabetes, Alzheimer's, and cancer. Because of the higher stability and predictability than with greater mRNA, this relatively small class of biomolecules becomes increasingly important in disease diagnosis and prognosis. However, the sequence homology, broad abundance, and common secondary structures of miRNA complicate efforts to develop accurate unbiased quantification techniques. Applications in discovery and clinical applications require flexibility in high efficiency processing, an extensive code library for multiple analysis, and custom analysis development. Microarray schemes provide high sensitivity and multiplexing performance but are not ideal for clinical use due to low throughput, complexity, and fixed design. PCR-based strategies also have significant throughput issues, require long optimization for multiplexing, and are only semi-quantitative. Existing bead-based systems provide high sample throughput (> 100 samples per day) but lack sensitivity, dynamic range, and multiplexing performance. Thus, there is a need for improved methods for detecting and quantifying nucleic acids such as miRNAs.

Multiple detection of miRNAs or any other biomolecules requires the ability to encode the substrate to which each molecule is linked. There are approximately two classes of techniques, planar arrays and suspension (particle-based) arrays that can be applied to multiplexing, both of which have application specific advantages. Planar arrays are absolutely dependent on location coding, and suspension arrays utilize a number of coding schemes that can be classified spectroscopically, graphically, electronically or physically.

Spectroscopic coding encompasses any manner that depends on the use of a particular light wavelength or radiation (including phosphors, chromophores, optical structures, or Raman tags) to identify species. Fluorescence-encoded microbeads can be processed quickly using conventional flow cytometers (or optical-fiber arrays), becoming a common form of multiplexing platform. Most spectroscopic coding methods rely on encapsulating detectable entities for coding, which can be a very challenging task depending on the substrate used.

There is a need for a more robust and generally-applicable coding method that allows for fast general purpose coding of substrates for multiplexed detection.

The present invention provides improved methods and compositions for nucleic acid detection and quantification that are multiplicityd, robust and reproducible with significant efficiency. The present invention is based, in part, on the discovery that post-hybrid labeling techniques can be applied to rapid and high-performance nucleic acid detection and / or quantification with a suitable fluid flow scanning or static imaging system. Surprisingly, the present post-hybrid labeling approach, when used with the multipurpose particle coding method, provides multiplexing scalability and atomomol sensitivity in a simple workflow. As described in detail below, using this powerful platform, miRNA expression profiles can be accurately analyzed for various types of cancers within 3 hours of low-input total RNA. Although miRNAs have been used by way of example, the methods and compositions according to the invention can be used to detect any nucleic acids (eg, DNA, RNA) or other types of specimens. Accordingly, the present invention provides a significant advance in the field of multiplexed biomolecule detection and quantification.

In one aspect, the present invention provides a substrate comprising at least one region having one or more nucleic acid probes, wherein the binding of both the target nucleic acid and the universal adapter to the same nucleic acid probe is characterized in that each is detectable by post-hybrid labeling. A nucleic acid probe consists of a capture sequence that binds a target nucleic acid and a contiguous adapter sequence that binds a universal adapter.

In one aspect, the invention provides a nucleic acid consisting of a capture sequence that binds a target nucleic acid and a contiguous adapter sequence that binds a universal nucleic acid such that binding of both the target nucleic acid and the universal adapter to the nucleic acid probe is detectable by post-hybrid labeling. Provide a probe.

In one aspect, the invention provides a substrate comprising one or more universal coding regions, wherein each universal coding region has one or more single-stranded polynucleotide templates, each template having a stem-loop structure and a stem-loop structure Consisting of a predetermined nucleotide sequence adjacent to.

First of all, the present invention provides a method for detecting the presence and / or number of target nucleic acids in a sample. In some embodiments, the method comprises: contacting a sample with a plurality of nucleic acid probes each consisting of a capture sequence that binds a target nucleic acid and a contiguous adapter sequence that binds a universal adapter; Culturing the plurality of probes and the sample under conditions in which one or more universal adapters are present and both individual target nucleic acids and individual universal adapters can be bound to the same individual nucleic acid probe; Conducting the reaction so that the individual universal adapters are combined with the individual target nucleic acids, and hybridizing with the same individual nucleic acid probe; And detecting the presence of one or more general purpose adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of target nucleic acids in the sample.

First of all, the present invention provides a substrate coding method. In some embodiments, such a method comprises: providing a substrate comprising one or more coding regions, each having one or more single-stranded polynucleotide templates; The labeled single-stranded coding adapter each comprising a sequence designed to specifically bind to an individual polynucleotide template, the labeled single-stranded coding adapter providing a plurality of labeled and unlabeled single-stranded coding adapters comprising a detectable substance; Culturing the substrate and a plurality of labeled and unlabeled single-stranded adapters under conditions such that the individual encoded adapters can bind to the single-stranded polynucleotide template; And binding the individual encoding adapters to the polynucleotide template of interest, thereby encoding the substrate.

Also provided are target nucleic acid detection kits. In some embodiments, such a kit comprises: a plurality of nucleic acid probes comprising a capture sequence that binds a target nucleic acid of interest and a contiguous adapter sequence that binds a universal adapter; And one or more general purpose adapters.

As used herein, "or" means "and / or" unless stated otherwise. As used herein, the term "comprising" and variations thereof such as "comprising" and "comprising" do not exclude other additions, elements, integers or steps. As used herein, the terms "about" and "approximately" Apply equally. Any numerical value used herein, with or without about / approximately, includes any normal variation that would be understood by one of ordinary skill in the art. In which "about" or "approximately" refer to 25%, 20% in both directions (increasing or decreasing) of the referenced reference value (except above 100%) unless stated otherwise or apparent in an isolation context. , 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3 Reference is made to numerical ranges falling within%, 2%, 1%, or below.

Other features, objects, and advantages of the invention will be apparent from the following detailed description, drawings, and claims. It is to be understood, however, that the description, drawings, and claims that represent embodiments of the invention are illustrative only and not intended to be limiting. Various modifications and changes that fall within the scope of the invention will be apparent to those skilled in the art.

The drawings are illustrative rather than restrictive.
1 is an exemplary diagram for general purpose coding and functionalization. (a) Hydrogel particles are prepared such that several universal coding regions each having a stem-loop structure and a unique 4bp sequence adjacent to the stem-loop, and a universal anchor in the probe region. In the ligase reaction, coding adapters are added in varying proportions to achieve the desired fluorescence level in each region, and probes are added along with the linker sequence to impart functionalization to the particle probe region. (b) Example of two batches of particles with unique cords and probes made using a universal particle set and various connection adapters.
FIG. 2 is an exemplary diagram of general purpose coding using multiple phosphors to encode particles or substrates into one or more colors (or otherwise functional species). Multiple adapter variants, each with inherent emission spectroscopy, can be applied. Each color level can be modulated by adjusting the respective adapter variant ratios to exhibit a unique signature of the plurality of fluorescent colors in the encoded regions of the particles.
3 is an exemplary diagram of probe-region functionalization by 3-species ligation, 2-species ligation, and chemical modification.
4 is an exemplary diagram utilizing probe-specific templates and polymerases to impart functionality to particles or substrates. Universal anchors (in this case there are two different anchors) are used with linkers having specific regions and probe sequences in one anchor. The polymerases stretch the anchors along the linker and functionalize the particles / substrates in one or multiple regions.
5 is an exemplary diagram of scanning multi-colors with a flow cytometer.
6 is an exemplary diagram of a single-color scan with a fluid flow-through instrument.
FIG. 7 is an exemplary fluorescence scattering plot for multiple functional particles having a single encoded region functionalized with four distinct levels of Cy3 (indicated in channel 2) and Cy5 (channel 4).
8 illustrates an example encoded gel particle analysis system. (a) the platform workflow includes (i) hybridization of particles and targets, (ii) incubation with particles and universal labeling adapters, ligase, and fluorescence reporters, and (iii) code identification and binding target content. Particles for scanning. Typical particles include a fluorescent barcode region and a probe-supported region separated by two inert portions. The central hole has a fixed value to indicate particle orientation. (b) Actual PMT fluorescence signatures of 75 flow-aligned particles in the 3-s scan segment. (c) Magnification markings for the individual particles in (b). Overlap scans were obtained on different days to show the analytical procedure reproducibility. The benchmark below the image is 50 um.
9 shows an exemplary high efficiency flow alignment mechanism and code design. (a) Photo of PDMS focal chamber attached to the pane, with inlets and outlets attached. The left reservoir inlet carries the sheath fluid and the central pipette tip carries the fluid with the particles. The right reservoir outlet serves as a recovery point for the scanned particles. The chamber is mounted on a standard inverted fluorescence microscope for scanning operation. (b) Photographs of particles used to optimize scanner performance. Simple plug particles were scanned to maximize signal-to-noise ratio (SNR) and detection circuit frequency response. Particles with holes of various areas were used to determine the minimum size difference needed to distinguish the code levels. Criteria are 50 um. (c) In the final particle design, the cord holes are 8 um apart and the lengths of the holes are 15, 27.5, and 40 um at levels 1, 2, and 3, respectively. All holes are 12 um wide.
10 is an exemplary diagram showing post-hybridized miRNA labeling via universal adapter and ligase reaction. (a) Coded Hydrogel Particles DNA probes aligned 5 'across the probe region are miRNA-specific adjacent to the universal adapter sequence such that the 3' end of the captured target is adjacent to the 5 'end of the captured adapter oligonucleotide. Has a sequence. The probe is capped with inverted dT to mitigate accidental linking enzyme reactions, and for efficient reporting the adapter has a poly (a) spacer so that the biotin binding 3 'end is away from the hydrogel. (b) After the particles hybridize with total RNA, T4 DNA streptavidin-phycoerythrin (SA-PE) is used as a fluorescence reporter. (c) This assay shows detection limits of about atomole at signal-to-noise = 3. (d) Single-nucleotide specificity is seen when 500 amol of synthetic let-7a RNA and particles with probes for let-7a, b, c, and d are added.
11 is an exemplary result showing relative ligase reaction efficiency over time. Error bars represent standard deviation of the five particle measurements.
FIG. 12 is an exemplary result showing the effect of universal adapter poly (A) tail length on fluorescence signal when biotin binding adapters are used with streptavidin-phycoerythrin reporter. The signals are relative values to those measured for tail length 12 bp.
13 shows exemplary direct labeling due to phosphor-binding adapters linked with ligase at the ends of the capture targets. Non-ligated adapters are washed out and particles are imaged (or scanned in a fluid flow mechanism). The fluorescence in the particles probe-area indicates the target content present.
Fig. 14 Exemplary multiplexed detection using multiple adapters with different fluorescent colors is shown. A given particle probe region may have several unique probes with common or different adapter sequences. Adapters with intrinsic emission spectroscopy (fluorescent or otherwise) phosphors are linked by ligase reactions, indicating the capture of multiple targets within a given probe region. The fluorescence intensity from each phosphor can be independently quantified to determine each target content present.
15 shows exemplary system efficiencies for 12-fold analysis. (a) Calibration curves for particle volumes represented by the plotted background-removal signal for spiked target content. miR-210, -221, -222 and let-7a were added to the same incubation mixes at the indicated content. The remaining seven naturally-occurring targets ('+' symbols) were added at 27- and 243-amol for efficiency verification. In all experiments, 200 ng of E. coli total RNA was also added to the complexity system. Considering target levels above 5 amol, the average COV of the target levels is 6.35%. Each point represents, on average, 19 particles that were single run. (b) let-7a probe specificity for the presence of sequences closely related to the intended target (see insertion box for target set). The highest cross-reactivity is around 27%. (c) Tumor profile results for four human tissues. Error bars represent the standard deviation measured three times for the same single-patient aliquot sample. Unless otherwise stated, the total RNA content used in the assay is 250 ng.
16 is an exemplary result showing detection calculation limits and correction curves for neat samples. (a) SNR extrapolation for determining the limit of detection (LOD). The LOD of the four calibration targets (see legend) was calculated to find the target content when the SNR was three. Regression lines with an average Pearson coefficient of 0.9965 (except miR-222) were used for LOD extrapolation. (b) Calibration curves for particle volumes cultured without E. coli total RNA added. Except for the presence of E. coli RNA, the conditions and those used to construct FIG. 3A are identical. (c) Comparison of background-removed signals by pure and E. coli calibration measurements. The point population around the identity line (red) means high specific detection without significantly reducing the binding rate in more complex samples. In all schemes, all target levels (except miSpike) were adjusted for comparison purposes by applying the background-rejected signal of the 100-amol miSpike profile.
17 illustrates exemplary dysregulation divisions. SNR was applied to distinguish regulatory abnormal targets from tissue profiles. The mean and standard deviation of the log-transformed expression rates were calculated for each target of each tissue analyzed three times. SNR 3 was selected as the threshold for anomaly regulation. All control over 20 cases were consistent with those described in the literature.
18 is an exemplary result showing a standard level of coefficient of variation (COV) as a function of the number of particles analyzed. The target level of COV for let-7a in the E. coli calibration scan appeared to stabilize to a nearly constant value in the 10-15 particle window for the five addition contents presented above.
19 is a conceptual illustrative diagram in which a scan for multi-functional particles is implemented. Standard cytometry records "phenomena" when the signal of the selected detector crosses a threshold, records single beads as single phenomena, and stores data for each channel. Multiple functional particles have functional regions provided with triggering materials (eg scattering induction) and single particles are recorded in multiple phenomena. By analyzing the shape and time-order of these phenomena and designing the particles appropriately, one can reconstruct this series of phenomena belonging to the same particle.
20 is an exemplary comparative diagram scanning fluorescence correction beads and multi functional particles. At least one phenomenon is recorded for the particle design (top), the recorded phenomena at each 1 ms time stamp (middle), and for the multi-functional particles having correction beads and two fluorescent regions. The distribution (bottom) of phenomena per time stamp is shown.
21 illustratively shows the design and use of a base set of test particles to assess scan alignment and consistency.
22 is an exemplary result of a basic set of test particles for assessing scan alignment and consistency.
FIG. 23 is an exemplary result of nucleic acid detection using particles having a single wide fluorescence region and narrow probe region representing “barcode”.
24 is an exemplary result of average scan along particle length (averaged over half width). The bottom signal, the second signal from the bottom, the second signal from the top, and the top signal correspond to 12.5%, 25%, 50%, and 100% of the fluorescent ligation mixture, respectively.
25 shows a) particle design and image for each mixture; And b) an average scan for five particles for each mixture. (1 um to 3.3px, numbers in the legend represent F1 and F2)
Figure 26 is an exemplary result of the measured fluorescence versus adapter content of each ligation reaction mixture.
27 illustrates an exemplary generic particle design for general purpose coding.
FIG. 28 shows exemplary fluorescent signals obtained in the barcode 1 region with various ratios of non-fluorescent adapters to fluorescence (Cy3).
29 shows an exemplary schematic of phenomena associated with barcoded gel particles. The YEL fluorescence (applied to barcodes) vs. RED2 fluorescence (applied to triggers) schemes are shown on the left and the YEL fluorescence (applied to barcodes) vs. GRN fluorescence (applied to orientation) schemes are shown on the right.
FIG. 30 shows an example for 25-time encoding using five intrinsic levels of YEL fluorescence in both barcode 1 and barcode 2 regions of encoded particles. These data were reconstructed from raw phenomena saved as FCS files in Guava software.
FIG. 31 is an example showing Atomol sensitivity (left),> 3 log dynamic range (left), and single-nucleotide specificity (right) using Firefly BioWorks' on-demand assay for microRNA targets. Firefly's 3-hour assay (total RNA results) to detect dilutions of 11 microRNA targets added to 250 ng of E. coli total RNA and report mean detector signal-to-addition in inter-run COV (inset) ) Was used. Specificity was assessed by adding a let-7a RNA target sample to the particles carrying probes for let-7a, 7b, 7c, and 7d where only one or two nucleotides each differed (right).
32 depicts an exemplary multiplexed isothermal amplification and capture assay for panel-based pathogen detection. Fluorescence amplification products generated by applying reverse transcription helicase-dependent amplification (RT-HDA) are captured to the encoded hydrogel particles in a single step. Each particle with three markings for a given species and probe regions with porosity formed to exclude helicase penetration can be immediately scanned in the microstructure without washing. High sensitivity and two-level specificity (amplification and hybridization) to the encoded gel particles can mitigate false-positive and negative judgments.
FIG. 33 shows an example of a concept-validated one-pot assay using standard PCR and isothermal amplification to show amplification specificity and sensitive detection of ˜11 template copies. Amplification specificity of the two targeting regions of lambda-phage DNA was assessed using single-vessel reactions with probes designed for amplification products generated by two separate primer sets. Amplification products could be detected with only ~ 11 copies, but -11,000 copies were added to the template lambda-phage (+) samples for (right) specificity testing. For specificity for human genomic DNA, human genome DNA-11,000 copies were added to the reaction in the absence of lambda-phage.
34 depicts an exemplary amplification primer (left) and amplification probe (right) design for multiple detection assays. Forward primers have a single Cy3 phosphor. The probes are designed to avoid 3'-extension that is accidental with 3 'phosphorylation with a higher T _m than the primers.
35 shows an exemplary design for barcoded gel particles for species-specific amplification product quantification.

In order to more easily understand the present invention, certain terms are first defined below. Additional definitions of the following terms and other terms are set forth throughout the specification.

In order to more easily understand the present invention, certain terms are first defined below. Additional definitions of the following terms and other terms are set forth throughout the specification.

"Adjacent" : As used herein, the term "adjacent" means "adjacent,""adjacent,""facing each other", "facing" or having a common boundary.

"Sample" : As used herein, the term "sample" means any substance that is to be analyzed, detected, measured, or quantified inclusively. Sample examples include, but are not limited to, proteins, peptides, hormones, haptens, antigens, antibodies, receptors, enzymes, nucleic acids, polysaccharides, chemicals, polymers, pathogens, toxins Fields, organic drugs, inorganic drugs, cells, tissues, microorganisms, viruses, bacteria, fungi, algae, parasites, allergens, contaminants, and combinations thereof.

"Linked ": As used herein, the terms "linked", "complexed", "coupled", "attached", "complexed", and "continuous", and grammatical equivalents, are typically two or more residues. Moieties are linked directly or indirectly to each other (eg, through one or more additional moieties that function as binders) to form a sufficiently stable structure, the moieties being the conditions under which the structure is used, e.g. For example , they remain connected when used in physiological conditions. In some embodiments, the residues are linked to each other by one or more covalent bonds. In some embodiments, the residues are linked to each other by a mechanism involving specific (but non-covalent) binding ( eg, streptavidin / avidin interaction, antibody / antigen interaction, etc. ). Alternatively or in addition, a sufficient number of weaker interactions (non-covalent) provide sufficient stability to keep the residues linked. Exemplary non-covalent interactions include, but are not limited to, affinity interactions, metal coordination, physical adsorption, host-customer interactions, hydrophobic interactions, pi lamination interactions, hydrogen bond interactions, van der Wils interactions, magnetic Interactions, electrostatic interactions, dipole-dipole interactions, and the like .

“Biomolecules ” : As used herein, the term “biomolecules” refers to molecules ( eg , proteins, amino acids, peptides, polynucleotides, nucleotides, carbohydrates, sugars, lipids, nucleoproteins). , Glycoproteins, lipoproteins, steroids, etc.) and may be commonly found in cells and tissues and may be naturally-occurring or artificially synthesized ( eg , by synthetic or recombinant methods). Certain groups of biomolecules include, but are not limited to, enzymes, receptors, neurotransmitters, hormones, cytokines, cellular response regulators such as growth factors and chemotactic factors, antibodies, vaccines, haptens , Toxins, interferons, ribozymes, anti-sense agents, plasmids, DNA, and RNA.

" Biocompatibility ": As used herein, the term "biocompatibility" means a substance that does not cause a substantially harmful reaction in vivo. In some embodiments, about 50%, about 45%, about 40%, about 35%, about 30%, about 25%, about 20%, about 15%, about when added to cells in vitro or in vivo 10%, about 5%, or about 5% or less apoptosis material is considered to be "biocompatible".

" Biodegradable " : As used herein, the term "biodegradable" means a substance that degrades under physiological conditions. In some embodiments, the biodegradable material is a material that is degraded by cellular mechanisms. In some embodiments, the biodegradable material is a material that is degraded by chemical treatment.

"Complementary": As used herein, the terms "complementary", "complementary" and "complementary" mean pairing of nucleotide sequences according to the Watson / Click pairing rule. For example, sequence 5'-GCGGTCCCA-3 'has complementary sequence 5'-TGGGACCGC-3'. The complementary sequence can also be an RNA sequence complementary to the DNA sequence. Certain bases not commonly found in natural nucleic acids can be included in complementary nucleic acids including, but not limited to, indosin, 7-diazaguanine, locked nucleic acids (LNA), and peptide nucleic acids (PNA). Complementarity need not be complete; Stable double strands may have mismatched base pairs, may have degenerative, or unmatched bases. Those skilled in the nucleic acid art can determine double strand stability experimentally by considering several variables including, for example, oligonucleotide length, oligonucleotide base composition and sequence, ionic strength and mismatched base pair frequencies.

"Concurrent" and "non-simultaneous" : As used herein, the terms "simultaneous,""simultaneously" or grammatical equivalents are used to describe multiple phenomena simultaneously without detectable or discernible sequential order. It means to happen or to happen. As used herein, the terms “non-simultaneous,” “non-simultaneous,” or grammatical equivalents mean that multiple phenomena occur or occur in a sequential order that is detectable or identifiable.

" Crude " : As used herein, the term "crude" when used in connection with a biological sample means a sample that is substantially in an unpurified state. For example, the crude sample may be a cell lysate or biopsy tissue sample. The crude sample can be a solution or a dry sample.

"Coded Region,""CodeRegion," or "Barcode Region" : The terms "coding region,""coderegion,""barcoderegion", or grammatical equivalents, as used herein, refer to an object or substrate (eg , Particle) means an area on the subject or substrate (eg, particle) used to identify. These terms may be used interchangeably. Typically, the encoded region of the subject has graphical and / or optical features associated with the subject identification. Such schematic and / or optical features are also referred to as signature features of the object. In some embodiments, an encoded region of an object is formed of spatial patterning features (eg, strips of various shapes and / or dimensions, or of varying size) that produce variable fluorescence intensities (of one or multiple wavelengths). A series of holes). In some embodiments, the encoded region of the object may be of various types and / or amounts of phosphors or other in various spatial patterns causing variable fluorescent signals (eg, different colors and / or intensities) in various patterns. Has detectable moieties.

"Functionalization: As used herein, the term" functionalization "refers to any process of modifying a substance by inducing physical, chemical or biological properties that are different from those found in the original substance. The functional groups used herein are groups of specific atoms that are in the molecules and cause the characteristic chemical reactions of these molecules.The functional groups used herein are chemical (eg, esters, carboxylates, alkyls) and Biological groups (eg, adapter, or linker sequences).

" Hybridization ": As used herein, the term "hybridization" or "hybridization" refers to the process by which two complementary nucleic acid strands are slowly cooled to each other under suitable stringent conditions. Oligonucleotides or probes suitable for hybridization are typically 10-100 nucleotides in length (eg, 18-50, 12-70, 10-30, 10-24, 18-36 nucleotides in length). Nucleic acid hybridization techniques are well known in the art. See, for example, Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, NY. Those skilled in the art will stably hybridize sequences with the desired level of complementarity, A lower complementarity sequence can understand how to estimate and adjust the stringency of hybridization conditions so that it does not. Examples of hybridization conditions and factors include, for example, Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, NY; Ausubel, FM et al. 1994, Current Protocols in Molecular Biology. John Wiley & Sons, Secaucus, NJ

" Hydrodynamic Diameter ": As used herein, the term "hydrodynamic diameter" generally refers to the effective diameter of a hydrating molecule (eg, macromolecules, colloids, or particles) in solution, which is the same in solution. Corresponds to the diameter of the sphere with mobility. In some embodiments, the hydrodynamic diameter is used to describe the particle size measured in solution. In certain embodiments, the hydrodynamic diameter is determined by may be determined by dynamic light scattering size measurement. For example, a Zetasizer Nano ZS instrument (Malvern) is used to measure the hydrodynamic diameters of the particles, as in the examples below.

"Inert region": As used herein, the terms "inert region,""inertspacer," or grammatical equivalents, when used in connection with an area of an object (eg, particle), include a fluid flow scanning device such as By a flow cytometer it is meant a region that is not detected above a predetermined trigger threshold. Typically, the inactive region or spacer is a non-functionalized region. For example, the inert region is a region free of probes or other detectable material.

" Interrogate " : As used herein, the terms "investigation", "query", "inspection" or grammatical equivalents refer to a characterization or inspection process for data acquisition.

"Cover": As used herein, the terms “labeling” and “labeling with a detectable agent or substance” are used interchangeably to form , for example , an entity after being combined with another entity ( eg , nucleic acid, polypeptide, etc. ). ) ( Eg , nucleic acid probes, antibodies, etc. ) can be visualized. The detectable preparation or substance is selected from generating a signal that is (eg proportional to) measurable and intensity related to the bound individual content. A wide range of systems are known in the art for labeling and / or detecting proteins and peptides. Labeled proteins and peptides are prepared by carrying or linking a label detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical, chemical or other means. The label or labeling substance is detectable directly ( ie , no further reaction or manipulation is required to be detectable, eg the phosphor is detectable directly) or indirectly detectable ( ie , with a reaction or other detectable entity). Detectable via binding, eg, hapten can be detected by immunopathologic staining after reaction with a suitable antibody comprising a reporter such as a phosphor). Suitable detectable preparations include, but are not limited to, radionucleotides, phosphors, chemiluminescent agents, microparticles, enzymes, colorimetric labels, magnetic labels, haptens, molecular beacons, aptamer beacons, and other And the like.

" Monodispersion ": As used herein, the terms " monodispersion " or " same size " mean substantially the same size and shape when referring to particles and have substantially the same weight when associated with polymers. Means a set of objects. In contrast, a set of subjects with inconsistent size, shape, and weight is called polydispersity. Monodisperse particles are typically synthesized using template-based synthesis.

" Subject " or "substrate" : As used herein, the terms "subject" and "substrate" are used interchangeably to refer to any discrete substance. The subject or substrate is particles, beads, planar surfaces, phages, macromolecules, cells, microorganisms, and the like.

" Particle ": As used herein, the term "particle" refers to a discrete subject. Such subjects can have any shape or size. The composition of the particles can vary depending on the application and the method of synthesis. Suitable materials include, but are not limited to, plastics, ceramics, glass, polystyrene, methylstyrene, acrylic polymers, metals, paramagnetic materials, toria sol, graphite carbon, titanium dioxide, latex or cross-linked dextran eg ceraroose, cellulose , Nylon, cross-linked micelles and teflon. In some embodiments, the particles are optically or magnetically detectable. In some embodiments, the particles have a fluorescent or luminescent material, or other detectable material. In some embodiments, particles having a diameter of 1000 nanometers (nm) or less are also referred to as nanoparticles.

" Polynucleotide ", " nucleic acid ", or " oligonucleotide ": The terms "polynucleotide", "nucleic acid", or "oligonucleotide" means a polymer of nucleotides. The terms "polynucleotide", "nucleic acid", and "oligonucleotide" may be used interchangeably. Typically, a polynucleotide has at least three nucleotides. DNA and RNA are polynucleotides. The polymer may be a natural nucleoside ( ie , adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine), nucleoside analogues ( eg For example , 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, C5-propynylcytidine, C5-propynuriridine, C5-bromouridine, C5- Fluorouridine, C5-iodouridine, C5-methylcytidine, 7-diazadenosine, 7-diazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O (6) -methylguanine, And 2-thiocytidine), chemically modified bases, biologically modified bases ( eg , methylated bases), insertion bases, modified sugars ( eg , 2'-fluororibose, ribose, 2'- deoxy-ribose, arabinose, and hexose), or modified phosphate groups (e. g., phosphorothioate and 5'-phospho-N- lamina Deet connection) the PO The.

"Probe" : As used herein, the term "probe" refers to a DNA or RNA fragment of variable length (eg, 3-1000 bases in length) and is used to detect the presence of target nucleotide sequences that are complementary to the probe sequence. do. Typically, the probe hybridizes with single-stranded nucleic acids (DNA or RNA) capable of probe-target base pairs due to the base sequence by complementarity between the probe and the target.

"Secondary structure" : As used herein, the term "secondary structure", when used in connection with a nucleic acid structure, refers to any structure formed by base pair interactions within a single molecule or within a collection of interacting molecules. Exemplary secondary structures include stem-loops or double helices.

"Signal": As used herein, the term "signal" means a detectable and / or measurable entity. In certain embodiments, the signal is visually detectable, eg visible. For example, the signal can be or related to the intensity and / or wavelength of the color in the visible spectrum. Non-limiting examples of such signals include colored precipitates and colored soluble products by chemical reactions such as enzymatic reactions. In certain embodiments, the signal can be detected using the device. In some embodiments, the signal is due to a phosphor that emits fluorescence when excited, wherein the fluorescence is detectable with a fluorescence detector. In some embodiments, the signal is or is associated with a spectrophotometer detectable light ( eg , visible light and / or ultraviolet light). For example, the light generated by the chemiluminescent reaction can be used as a signal. In some embodiments, the signal is, for example, is associated or radiation emitted by the radioisotope, infrared, and so on. In certain embodiments, the signal is a direct or indirect indicator of the characteristics of the physical entity. For example, the signal can be used as an indicator of nucleic acid content and / or concentration in biological samples and / or reaction vessels.

"Specific" : As used herein, the term "specific", when used in connection with an oligonucleotide primer, may hybridize with the target of interest and does not substantially hybridize with the non-interested nucleic acids under suitable hybridization or wash conditions. Oligonucleotide or primer. Higher levels of sequence identity are preferred and include at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity. In some embodiments, a specific oligonucleotide or primer is at least 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, with a portion of the nucleic acid that hybridizes or amplifies when the oligonucleotide and nucleic acid are aligned. Has sequence identity of 24, 26, 28, 30, 35, 40, 45, 50, 55, 60, 65, 70, or more bases.

" Stem -loop" : As used herein, the term "stem-loop", when used in connection with a nucleic acid structure, refers to a structure due to intramolecular base pairing that typically occurs in single-stranded DNA or RNA. This structure is also known as hairpins or hairpin loops. Typically, this occurs when two regions of the same strand where the nucleotide sequence is normally complementary when read in the opposite direction end in a base-paired, unpaired loop to form a double helix leading to a lollipop-shaped structure. .

"Substantially " : As used herein, the term "substantially" means quantitative conditions that exhibit a complete or near-complete degree of characteristic or property of interest. One of ordinary skill in the biological arts can understand that biological and chemical phenomena rarely progress completely and / or are fully performed or to achieve or avoid absolute results. The term "substantially" as used herein, therefore, takes into account the potential lack of integrity specific to many biological and chemical phenomena.

"Substantially Complementary" : As used herein, the term "substantially complementary" refers to two sequences that have degree of hybridization under stringent hybridization conditions. Those skilled in the art will appreciate that substantially complementary sequences need not be hybridized along the entire length. In some embodiments, “strict hybridization conditions” means stringent hybridization conditions, at least as follows: 50% formamide, 5XSSC, 50 mM NaH ₂ PO ₄ , pH 6.8, 0.5% SDS, 0.1 mg / mL grinding Hybridized salmon sperm DNA, and overnight at 42 ^° C. in 5 × Denhart solution; Washed with 2XSSC, 0.1% SDS at 45 ^o C; And washed with 0.2 × SSC, 0.1% SDS at 45 ^° C. In some embodiments, stringent hybridization conditions do not hybridize two nucleic acids that differ by two or more bases over 20 contiguous nucleotides.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides, among other things, methods and compositions for the detection and quantification of target nucleic acids by post-hybrid labeling. In some embodiments, the present invention provides a method for detecting the presence and / or number of target nucleic acids in a sample, wherein (a) each comprises a capture sequence that binds to the target nucleic acid and a contiguous adapter sequence that binds to a universal adapter Contacting the plurality of nucleic acid probes and the sample; (b) culturing the plurality of probes and the sample under conditions in which one or more universal adapters are present and both the individual target nucleic acid and the individual universal adapter can bind to the same individual nucleic acid probe; (c) conducting a reaction in which individual universal adapters and individual target nucleic acids can bind, wherein they hybridize with the same individual nucleic acid probe; (d) detecting the presence of one or more general purpose adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of target nucleic acids in the sample. Typically, universal adapters are labeled with detectable moieties or other labeling groups that facilitate detection. In some embodiments, a plurality of nucleic acid probes suitable for the present invention are attached to a substrate or object (eg, microarray, or particle).

It is also contemplated that such a ligation-based mode (or other binding mode) can be used to encode or otherwise functionalize various subjects or substrates (eg, particles). Thus, in some embodiments, the present invention provides methods and compositions for general purpose coding. In certain embodiments, the present invention provides a method of encoding a subject (eg, a particle), wherein (a) a subject comprising one or more coding regions each bearing one or more single-stranded polynucleotide templates Or providing a substrate (eg, particle); (b) each of the single-stranded coding adapters having a sequence designed to specifically bind to a polynucleotide template, detectably labeled (eg, labeled with phosphors or other detectable substances) and unlabeled Providing a blend; (c) culturing the subject and the encoding adapters under conditions in which the individual encoding adapters are associated with the corresponding polynucleotide templates; And (d) binding the encoding adapters with the corresponding polynucleotide templates, thereby encoding the subject or substrate. In some embodiments, the amount of labeled adapter to (vs) unlabeled adapter (having the same or similar sequences) can be varied to control the amount of signal (eg, fluorescence) generated in each encoded region. Alternatively or additionally, subjects or substrates (eg, embedded) with nucleic acid anchors embedded in the probe region to attach the desired probes to functionalize the probe region of the subjects or substrates (eg particles). Particles) can be used. In this way, coding and probe functionalization can be achieved in a single reaction.

Thus, the methods according to the present invention are in a general-purpose architecture for batches of objects (eg particles) having unique codes and probes from a single amount of objects (eg particles). Can be prepared). In the case of highly multiplexed identification, this approach saves manufacturing time and cost compared to synthesizing particle quantities independently for each target. Importantly, the particles produced by the method can also be applied in a post-hybrid labeling manner for the highly efficient nucleic acid (eg, microRNA) detection and quantification described herein.

Various aspects of the invention are described in more detail in the following subsections. The description in details is not a limitation of the present invention. Each detail may apply to any aspect of the present invention. As used herein, "or" means "and / or" unless stated otherwise.

Nucleic Acid Probes for Post-Hybrid Labeling

Nucleic acid probes suitable for the present invention are designed to generate a detectable signal indicative of the presence and capture of nucleic acid targets, such as miRNA targets. Thus, in some embodiments, a nucleic acid probe suitable for the invention comprises a capture sequence that binds the target nucleic acid of interest and a contiguous adapter sequence that binds a universal adapter. According to the present invention, the capture sequence and the adapter sequence are configured such that both the target nucleic acid and the universal adapter are coupled to the nucleic acid probe so that the universal adapter is linked to the target nucleic acid. In some embodiments, when both the target nucleic acid and the universal adapter are bound to the nucleic acid probe, the 3 'end of the target is adjacent to the 5' end of the universal adapter. In some embodiments, when both the target nucleic acid and the universal adapter are bound to the nucleic acid probe, the 5 'end of the target is adjacent to the 3' end of the universal adapter. In some embodiments, the universal adapter is linked, bound, attached or coupled to the target nucleic acid by enzyme or chemical bond. In some embodiments, DNA or RNA ligase is used to link the universal adapter to the target nucleic acid. In some embodiments, a T4 DNA ligase is used to link the universal adapter to the target nucleic acid. In some embodiments, a common, detectable universal adapter can be used to label multiple targets in a single reaction.

Capture sequence

In some embodiments, a suitable capture sequence is specific for the target nucleic acid (eg, DNA, mRNA, or microRNA). The term “specific”, when used in connection with a hybridization probe, refers to a sequence that binds to a target in stringent conditions but not to other regions.

For example, a suitable capture sequence has a sequence that is substantially complementary to the target sequence of the target nucleic acid, eg, microRNA. Typically, capture sequences are based on target-specific nucleotide sequences. In some embodiments, the capture sequence is, for example, a microRNA that indicates a given cancer, diabetes, Alzheimer's or other diseases, but not limited to let-7a, miR-21, miR-29b-2, miR-181b -1, miR-143, miR-145, miR-146a, miR-210, miR-221, miR-222, miR-10b, miR-15a, miR-16, miR-17, miR-18a, miR-19a , miR20a, miR-1, miR-29, miR-181, miR372, miR-373, miR-155, miR-101, miR-195, miR-29, miR-17-3p, miR-92a, miR-25 It has a sequence substantially complementary to the microRNA specific sequence of interest, including, miR-223, miR-486, miR-223, mir-375, miR-99b, miR-127, miR-126, miR-184.

In some embodiments, suitable capture sequences are designed to distinguish different different species of target nucleic acids. The present invention is particularly useful for distinguishing multiple species of target nucleic acids having identical sequences at one end and variable sequences at the other end. Thus, in some embodiments, the capture sequence is designed complementary to the desired variable terminal nucleotide sequence. Only by binding to the desired target species, there is a complete 3 'end consensus to be adjacent to the 5' end of the adapter sequence, thereby allowing the target to undergo ligase reaction with the adapter. Thus, universal adapter detection associated with a probe can indicate the presence of a target nucleic acid of desired terminal variability in a sample. In certain embodiments, the present invention can be applied to distinguish precursor-microRNAs and mature microRNAs. Typically, precursor-microRNA and mature microRNA have the same 5 'region and distinct 3' region due to 3 'arm cleavage in precursor form during maturation. To specifically detect the mature microRNA, the capture sequence is designed to be substantially complementary to the 3 'terminal sequence of the mature microRNA. Thus, only by binding to the exact mature microRNA and capture sequence, the 3 'end of the microRNA is exactly matched so as to be adjacent to the 5' end of the adapter sequence, so that the adapter sequence can be linked to the target sequence by ligase reaction.

In some embodiments, the capture sequence for nucleic acid targets is up to 50 nucleotides (eg, up to 25, 20, 18, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide). In some embodiments, the capture sequence is also selected so that the melting point Tm in the ligase buffer is 20-50 C.

Adapter sequence

In general, an adapter sequence can have any sequence and length. Typically, adapter sequences and lengths have a (1) melting point of about 10-20 C in the ligase buffer and (2) the sequence has significant self-complementation to avoid hairpins, other secondary structures or homodimer formation. And / or (3) complete DNA probes (with adapter and miRNA sequences) are designed to not form significant hairpins or other secondary structures. In some embodiments, a suitable adapter sequence may comprise up to 20 nucleotides (eg, up to 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide).

In some embodiments, a suitable nucleic acid probe has a 3 'cap to prevent or mitigate accidental ligase reaction. Exemplary suitable 3 ′ caps include, but are not limited to, inverse dT, or 3 ′ phosphorylation . In some embodiments, a suitable nucleic acid probe has a chemical anchor at the 5 'or 3' end and thus the probe is attached to the substrate. Suitable exemplary chemical anchor groups include, but are not limited to, carboxyl groups, amine groups, thiol groups, biotin, and / or azide groups. In some embodiments, a suitable probe may have a specific nucleic acid sequence that can be bound to a specific substrate or specific substrate location. Typically, this particular nucleic acid sequence is intended to be complementary to the capture sequence embedded at the desired substrate position. In some embodiments, capturing the nucleic acid probe at the desired location is associated with probe identification. Thus, these specific nucleic acid sequences are also referred to as nucleic acid barcodes.

Suitable probes are typically long enough to specifically hybridize with the target but not large enough to interfere with the hybridization process. The size depends on the desired melting point of the target-probe complex or the specificity required for target differentiation. In some embodiments, suitable probes are about 10-70 nucleotides (eg, 10-60, 10-50, 10-40, 10-30, 10-25, 10-20, 15-70, 15- 60, 15-50, 15-40, 15-30, 15-25, 20-70, 20-60, 20-50, 20-40, 20-30 nucleotides). Various methods and software in the art can be used to design specific probes.

Nucleic acid probes according to the present invention are natural nucleosides ( ie , adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine), nunudes Cleoside analogs ( eg , 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, C5-propynylcytidine, C5-propynuridine, C5-bromo Uridine, C5-fluorouridine, C5-iodouridine, C5-methylcytidine, 7-diazadenosine, 7-diazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O (6 ) -Methylguanine, and 2-thiocytidine), chemically modified bases, biologically modified bases ( eg , methylated bases), insertion bases, modified sugars ( eg , 2'-fluororibose, ribose, 2'-deoxy-ribose, arabinose, and hexose), or modified phosphate groups (eg, phosphorothioate and 5'-N- Force And a lamina Deet connection).

Universal adapter

According to the present invention, when the universal adapter is combined with a nucleic acid probe, a universal adapter suitable for the 5 'or 3' end of the adapter to be adjacent to the 3 'or 5' end of the target nucleic acid, respectively, is a sequence complementary to the adapter sequence of the nucleic acid probe. Has Suitable lengths and sequences of the universal adapter can be selected using methods well known and published in the art. For example, a suitable adapter may be 1-25 nucleotides in length (e.g., 1-20, 1-18, 1-16, 1-14, 1-12, 1-10, 5-20, 5-15, Or 5-10 nucleotides).

Adapters are DNA, RNA, or any type of nucleic acid analog. Nucleotides of the adapters may be native nucleosides ( ie , adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine), nucleoside analogs (e. g., 2-amino-adenosine, 2-thio-thymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, C5- propynyl cytidine, C5- propynyl uridine, C5--bromo-uridine, C5-fluorouridine, C5-iodouridine, C5-methylcytidine, 7-diazadenosine, 7-diazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O (6) -methyl Guanine, and 2-thiocytidine), chemically modified bases, biologically modified bases ( eg , methylated bases), insertion bases, modified sugars ( eg , 2′-fluororibose, ribose, 2 '-Deoxyribose, arabinose, and hexose), or modified phosphate groups ( eg , phosphorothioate and 5'-N-phospho Lamination connection).

In some embodiments, the general purpose adapter is biotinylated. In some embodiments, the biotinylated general purpose adapter is, but is not limited to, phycoetrine, PE-Cy5, PE-Cy5.5, PE-Cy7, APC, PerCP, quantum dots, phosphors or other described herein ( See also “detectable individuals” section) detected by streptavidin reporters bound to a detectable substance comprising detectable individuals. In some embodiments, the biotinylated universal adapter can be detected by a streptavidin reporter bound to the enzyme for enzyme signal generation. In some embodiments, suitable streptavidin reporters may be bound to alkaline phosphatase, beta-galactosidase, mustard peroxidase, or other enzymes capable of forming a detectable product. In some embodiments, enzyme signal generation may be indicated by chemiluminescence, fluorescence, or colorimetric detection (see Reference Detectable Subjects section). In some embodiments, the universal adapter has a nucleotide tail (also called a spacer or linker) that extends the biotin or enzyme group away from the gel matrix polymer backbone to avoid potential steric hindrance. Suitable nucleotide tails (spacers or linkers) may have various sequences. In some embodiments, poly (A) or poly (T) tails are used. In some embodiments, a suitable nucleotide (eg poly (A)) tail has up to 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 bases.

In some embodiments, the universal adapter is labeled directly with phosphors or other detectable entities (see section "Detectable Materials").

In some embodiments, multiple universal adapters are used to label multiple discrete target nucleic acids in a single reaction. Typically, in such cases, each individual universal adapter is detected by a biotin-streptavidin reporter system labeled or separated with detectable substances to distinguish.

Exemplary detectable entities suitable for the present invention are described below.

Detectable Objects ( Entities )

Any wide range of detectable preparations can be used to implement the present invention. Suitable detectable preparations include, but are not limited to: various ligands, radionuclides; Fluorescent dyes; Chemiluminescent agents (eg, acridinium esters, stabilized dioxetane, and the like); Bioluminescent preparations; Spectroscopically degradable inorganic fluorescent semiconductor nanocrystals (ie, quantum dots); Microparticles; Metal nanoparticles (eg, gold, silver, copper, platinum, etc.); Nanoclusters; Paramagnetic metal ions; Enzymes; Colorimetric labels (eg, dyes, gold colloids, and the like); Biotin; Deoxygenin; Haptens; And proteins in which antisera or monoclonal antibodies can be used.

In some embodiments, the detectable substance is biotin. Biotin can be bound (directly or indirectly) to avidin (eg streptavidin), which is usually combined with other detectable substances (eg fluorescent material).

Some non-limiting examples of other detectable materials are given below.

Fluorescent dyes

In certain embodiments, the detectable material is a fluorescent dye. Numerous known fluorescent dyes with various chemical structures and properties can be used in the implementation of the present invention. The fluorescent detectable material is stimulated by a laser so that the emitted light is captured by the detector. The detector is a charge coupled device (CCD) or confocal microscope and records the intensity.

Suitable fluorescent dyes include but are not limited to fluorescein and fluorescein line dyes (e.g. fluorescein isothiocyanine or FITC, naphthofluorescein, 4 ', 5'-dichloro-2', 7) '-Dimethoxyfluorescein, 6-carboxyfluorescein or FAM, etc.), carbocyanine, merocyanine, styryl dyes, oxonol dyes, phycoerythrin, erythrosine, eosin, rhodamine Dyes (e.g., carboxytetramethyl-rhodamine or TAMRA, carboxyrodamine 6G, carboxy-X-rhodamine (ROX), lysamine rhodamine B, rhodamine 6G, rhodamine green, rhodamine red, tetra Methylodamine (TMR), etc.), coumarin and coumarin based dyes (e.g., methoxycoumarin, dialkylaminocoumarin, hydroxycoumarin, aminomethylcoumarin (AMCA), etc.), oregon green dyes (E.g., Oregon Green 488, Oregon Green 500, Oregon Green 514., Etc.), Texas Red, Texas Red-X, Spectrum Red ^TM , Spectrum Green ^TM , Cyanine Dyes (eg, CY-3 ^TM , CY-5 ^TM , CY-3.5 ^TM , CY-5.5 ^TM , etc. ), ALEXA FLUOR ^TM dyes ^{(e.g., ALEXA FLUOR TM 350, ALEXA FLUOR} TM 488, ALEXA FLUOR TM 532, ALEXA FLUOR TM 546, ALEXA FLUOR TM 568, ALEXA FLUOR TM 594, ALEXA FLUOR TM 633, ALEXA FLUOR TM 660, ALEXA FLUOR ^TM 680, other, etc.), BODIPY ^TM The dyes (e.g., BODIPY FL ^{TM, TM} BODIPY R6G, BODIPY ^TM TMR, BODIPY ^TM TR, BODIPY ^TM 530/550, the ^{BODIPY TM 558/568, BODIPY TM 564/570,} BODIPY TM 576/589, BODIPY TM 581/591, BODIPY TM 630/650, BODIPY TM 650/665, etc etc.), IR dyes (e. Such as IRD40, IRD 700, IRD 800, etc.), and the like. Additional suitable fluorescent dyes examples and methods for binding fluorescent dyes to other chemical entities such as proteins and peptides, for example, see The Handbook of Fluorescent Probes and Research Products, 9th Ed., Molecular Probes. See, Inc., Eugene, OR. Fluorescent labeling aids include high molar absorption coefficients, high fluorescence quantum yields, and photostability. In some embodiments, the label phosphors show absorption and emission wavelengths in the visible region (ie 400-750 nm) rather than in the ultraviolet region (ie 400 nm or less).

Detectable substances include one or more chemical entities, for example in fluorescence resonance energy transfer (FRET). Resonance transition improves the emission intensity as a whole. For example, Ju et al. (1995) Proc. Nat'l Acad. Sci. (USA) 92: 4347. To achieve resonance energy transfer, the first fluorescent molecule ("donor" phosphor) absorbs light and transitions to the second fluorescent molecule ("acceptor" phosphor) through excitation electrons resonance. In one method, both the donor and acceptor dyes are linked together and attached to the oligo primer. Methods of linking donor and acceptor dyes to nucleic acids are described, for example, in Lee et al. Is already described in US Pat. No. 5,945,526. Donor / acceptor pairs of dyes that can be used are, for example, fluorescein / tetramethylhodamine, IAEDANS / fluorescein, EDANS / DABCYL, fluorescein / fluorescein, BODIPY FL / BODIPY FL, and fluorine Resins / QSY 7 dyes. See, eg, Lee et al. US Patent No. 5,945,526. Many of these dyes are also described, for example, in Molecular Probes Inc. Commercially available from (Eugene, Oreg.). Suitable donor phosphors include 6-carboxyfluorescein (FAM), tetrachloro-6-carboxyfluorescein (TET), 2'-chloro-7'-phenyl-1,4-dichloro-6-carboxyfluorescein ( VIC), and the like.

Suitable detectable materials may be insert DNA / RNA dyes that show a significant increase in fluorescence when combined with double-stranded DNA / RNA. Exemplary suitable dyes include, but are not limited to, SYBR ™ and Pico Green (Molecular Probes, Inc., Eugene, Oreg.), Ethidium bromide, propidium iodide, chromomycin, acridine orange, Hoechst 33258, Toto-1, Yoyo-1, and DAPI (4 ', 6-diimidino-2-phenylindole hydrochloride). Further description of the application of intercalating dyes is described in Zhu et al., Anal . Chem . 66: 1941-1948 (1994).

Enzymes

In certain embodiments, the detectable substance is an enzyme. Exemplary suitable enzymes include, but are not limited to, those used in ELISA, such as mustard peroxidase, beta-galactosidase, luciferase, alkaline phosphatase, and the like. Other examples include beta-glucuronidase, beta-D-glucosidase, urease, glucose oxidase, and the like. The enzyme can be linked to the molecule using a linker group such as carbodiimide, diisocyanate, glutaraldehyde, and the like.

Radioisotopes

In certain embodiments, the detectable substance is a radioisotope. For example, a molecule may be isotopically labeled (ie, including one or more atoms substituted with atoms having an atomic weight or mass number that is different from the atomic weight or mass number commonly found in nature), and isotopes may be attached to the molecule. Non-limiting examples of isotopes that may be bound to molecules include isotopes of hydrogen, carbon, fluorine, phosphorus, copper, gallium, yttrium, technetium, indium, iodine, rhenium, thallium, bismuth, asatin, samarium, and lutetium (Ie 3H, 13C, 14C, 18F, 19F, 32P, 35S, 64Cu, 67Cu, 67Ga, 90Y, 99mTc, 111In, 125I, 123I, 129I, 131I, 135I, 186Re, 187Re, 201Tl, 212Bi, 213Bi, 211At, 153Sm, 177Lu).

In some embodiments, signal amplification is accomplished using a labeled dendrimer as a detectable substance (see, eg, Physiol Genomics 3: 93-99, 2000, which is incorporated herein by reference in its entirety). Fluorescently labeled dendrimers are available from Genisphere (Montvale, N.J.). They can be chemically bound to oligonucleotide primers by methods known in the art.

Temperaments

In some embodiments, a nucleic acid probe suitable for post-hybrid labeling is attached to a substrate or subject. Suitable substrates or subjects may have planar, spherical, or non-spherical morphologies. Suitable substrates or subjects can be solid, semi-solid, polymer, emulsion, or the like. Suitable substrates or subjects include, but are not limited to, microspheres (eg, glass, polymers, etc.), genetically modified cells having microarrays, glasses, slides, particles, beads, films, membranes, inner or outer surfaces. Include cells, microorganisms (eg, pretty nematodes (eg, modified nematodes for drug testing), bacteria, yeasts, and / or fungi)

For illustrative purposes, particles are used in the various examples below.

Particles

Particles suitable for use in accordance with the present invention may be made of any material. Suitable particles may be biocompatible, non-biocompatible. Suitable particles can also be biodegradable or non-biodegradable.

Materials

In some embodiments, the particles are made of polymers. Exemplary polymers include but are not limited to poly (arylates), poly (anhydrides), poly (hydroxy acids), polyesters, poly (ortho esters), poly (alkylene oxides), polycarbonates, poly (propylene fumarates) , Poly (caprolactone), polyamide, polyamino acid, polyacetal, polylactide, polyglycolide, poly (dioxanone), polyhydroxybutyrate, polyhydroxyvalylate, poly (vinyl pyrrolidone), Polycyanoacrylates, polyurethanes and polysaccharides. In some embodiments, the polymers of particles comprise polyethylene glycol (PEG). In some embodiments, the polymers of particles are formed by stage or chain polymerization. The amount and type of radical initiators, such as photosensitive initiators (e.g. UV or infrared), thermosensitive initiators, or chemical initiators, or the amount of heat or light applied, can be used to control the reaction rate or to change the molecular weight. . If necessary, a catalyst can be used to speed up the reaction or to change the molecular weight. For example, strong acids can be used as catalysts in step polymerization. Trifunctional and other multifunctional monomers or crosslinking agents may be used to increase the crosslinking density. In chain polymerization, the chemical initiator concentration in the mixture of one or more monomers can be adjusted to manipulate the final molecular weight.

Exemplary methods for producing particles are described in US Pat. No. 7709544 and US Application Publication No. 20080176216, the entire contents of which are incorporated herein by reference. For example, the process may proceed with any polymerizable liquid-phase monomer, in which the form of particles suitable for use in the present invention are formed and polymerized in a single etch-polymerization step. Exemplary monomers are allyl methacrylate, benzyl methylacrylate, 1,3-butanediol dimethacrylate, 1,4-butanediol dimethacrylate, butyl acrylate, n-butyl methacrylate, diethylene glycol diacryl Ethylene, diethylene glycol dimethacrylate, ethyl acrylate, ethylene glycol dimethacrylate, ethyl methacrylate, 2-ethyl hexyl acrylate, 1,6-hexanediol dimethacrylate, 4-hydroxybutyl acryl Latex, hydroxyethyl acrylate, 2-hydroxyethyl methacrylate, 2-hydroxypropyl acrylate, isobutyl methacrylate, lauryl methacrylate, methacrylic acid, methyl acrylate, methyl methacrylate, Monoethylene glycol, 2,2,3,3,4,4,5,5-octafluoropentyl acrylate, pentaerythritol triacrylate, polyethylene glycol (200) diacrylate , Polyethylene glycol (400) diacrylate, polyethylene glycol (600) diacrylate, polyethylene glycol (200) dimethacrylate, polyethylene glycol (400) dimethacrylate, polyethylene glycol (600) dimethacrylate, Stearyl methacrylate, triethylene glycol, triethylene glycol dimethacrylate, 2,2,2-trifluoroethyl 2-methylacrylate, trimethylolpropane triacrylate, acrylamide, N, N, -methylene Bisacryl-amide, phenyl acrylate, divinyl benzene, and the like. In certain embodiments, the monomer is characterized by a polymerization reaction that terminates with terminating species. Terminating species, etch illumination, and monomer configurations can thus be chosen to be mutually considered to produce particles suitable for use in the present invention.

In some embodiments, the particles are hydrogels. In general, the hydrogels comprise substantially some crosslinked network. Water or other fluids may pass through the network forming the hydrogel. In some embodiments, hydrogels suitable for use in the present invention are made or include a hydrophilic polymer. For example, hydrophilic polymers include anionic groups ( eg phosphoric acid groups, sulfuric acid groups, carboxyl groups); Cationic groups ( eg quaternary amine groups); Or polar groups ( eg hydroxyl groups, thiol groups, amine groups). In some embodiments, the hydrogels are superabsorbents ( eg contain more than 99% water) and have a very similar softness to natural tissue due to the significant water content. At both weight and volume, the hydrogels are fluids in composition and thus exhibit a density of constituent liquid (eg water). The present invention encompasses the recognition that hydrogels are particularly useful in some embodiments of the present invention. Without being bound by any particular theory, hydrogels are readily implemented (eg, flow cytometers) without substantially modifying detection devices, especially devices purchased commercially (eg, flow cytometers), and 2) surface functionalization is required. It is contemplated that functional materials can be readily included (eg, in a single etch-polymerization step) without having to. Due to their bio-friendly properties, hydrogels are mainly used in the fields of tissue engineering, drug delivery and biomolecule separation.

Particles can be synthesized with a variety of additional materials and methods. In some embodiments, the particles are made or include one or more polymers. The polymers used in the particles may be natural polymers or artificial ( eg synthetic) polymers. In some embodiments, the polymers are linear or branched polymers. In some embodiments, the polymers may be dendrimers. The polymers may be homopolymers or copolymers comprising two or more monomers. In terms of the arrangement order, the copolymers may be block copolymers, graft copolymers, random copolymers, blends, mixtures, and / or additives of any of these and other polymers.

In some embodiments, the particles of the invention are made of or include a natural polymer such as carbohydrates, proteins, nucleic acids, lipids, and so on. In some embodiments, natural polymers can be made synthetically. Many natural polymers such as collagen, hyaluronic acid (HA), and fibrin derived from various components of the extracellular matrix of a mammal can be used as the particles of the present invention. Collagen is one of the major proteins of mammalian extracellular matrix, and HA is a polysaccharide found in almost all animal tissues. Alginates and agarose are polysaccharides derived from marine algae. Natural polymers are advantageous because of their low toxicity and high biocompatibility.

In some embodiments, the polymer is a carbohydrate. In some embodiments, the carbohydrate is a monosaccharide ( ie monosaccharide). In some embodiments, the carbohydrate may be a polysaccharide comprising disaccharides, oligosaccharides, and / or monosaccharides and / or derivatives thereof linked to glycosidic bonds known in the art. Although carbohydrates used in the present invention are typically natural carbohydrates, they can be at least partially-synthesized. In some embodiments, the carbohydrate is derived natural carbohydrate.

In certain embodiments, the carbohydrate is or includes monosaccharides, including but not limited to glucose, fructose, galactose, ribose, lactose, sucrose, maltose, trehalose, selvios, mannose, xylose, ara Vinose, glucononic acid, galactonic acid, mannuronic acid, glucosamine, galactosamine, and neuramic acid. In certain embodiments, carbohydrates are or include disaccharides and include, but are not limited to, lactose, sucrose, maltose, trehalose, and cellobiose. In certain embodiments, the carbohydrate is or includes polysaccharide, including but not limited to hyaluronic acid (HA), alginate, heparin, agarose, chitosan, N, O-carboxymethylchitosan, chitin, cellulose, crystalline cellulose , Hydroxypropyl methylcellulose (HPMC), hydroxycellulose (HC), methylcellulose (MC), pullulan, dextran, cyclodextran, glycogen, starch, hydroxyethyl starch, carrageenan, glycon, amylose, starch , Heparin, konjac, glucomannan, futuran, curdlan, and xanthan. In certain embodiments, carbohydrates are sugar alcohols and include, but are not limited to, mannitol, sorbitol, ziitol, erythritol, maltitol, and lactitol.

In some embodiments, the particles of the present invention are made of or include synthetic polymers, including but not limited to poly (arylate), poly (anhydride), poly (hydroxy acid), poly (alkylene oxide) , Poly (propylene fumerate), polymethacrylate polyacetal, polyethylene, polycarbonate ( e.g. poly (1,3-dioxan-2-one)), polyanhydrides ( e.g. poly (segrose anhydride) ), Polyhydroxy acids ( e.g. poly (β-hydroxyalkanoate)), polypropylfumarate, polycaprolactone, polyamides ( e.g. polycaprolactam), polyacetals, polyethers, polyesters ( E.g. Polylactide, polyglycolide, poly (dioxanone), polyhydroxybutyrate,), poly (orthoester), polycyanoacrylate, polyvinyl alcohol, polyurethane, polyphosphazene, polyacrylate, polymetha Acrylates, polyureas, polyamines and copolymers thereof. Exemplary polymers also include polyvalerolactone, poly (sebabacic anhydride), polyethyleneglycol, polystyrene, polyhydroxyvalylate, poly (vinyl pyrrolidone) poly (hydroxyethyl methacrylate) (PHEMA), poly ( Vinyl alcohol) (PVA), and derivatives and copolymers thereof.

In some embodiments, the polymers of particles are formed by stage or chain polymerization. The amount and type of radical initiators, such as photosensitive initiators (e.g. UV or infrared), thermosensitive initiators, or chemical initiators, or the amount of heat or light applied, can be used to control the rate of polymerization or to change molecular weight. . If necessary, a catalyst can be used to speed up the reaction or to change the molecular weight. For example, strong acids can be used as catalysts in step polymerization. Trifunctional and other multifunctional monomers or crosslinkers may be used to increase the crosslinking density of the polymers. In chain polymerization, the chemical initiator concentration in the mixture of one or more monomers can be adjusted to manipulate the final molecular weight.

In some embodiments, a photocrosslinking method can be applied to prepare the polymer particles according to the present invention. Upon exposure to light, photoinitiators form reactive free radical species which initiate monomer crosslinking and / or polymerization. Any photoinitiator can be used for the crosslinking and / or polymerization reactions. Photoinitiation polymerization and photoinitiator Rabek, Mechanisms of Photophysical Processes and Photochemical Reactions in Polymers , New York: Wiley & Sons, 1987; Fouassier, Photoinitiation, Photopolymerization , and Photocuring , Cincinnati, OH: Hanser / Gardner; Fisher et al . , 2001, Annu . Rev. Mater . Res . The photoinitiator produces free radicals at any light wavelength. In certain embodiments, the photoinitiator reacts in UV light (200-500 nm). In certain embodiments, UV long wavelength light is used. In other embodiments, UV short wavelength rays are used. In some embodiments, the photoinitiator is reacted using visible light (400-800 nm). In certain embodiments, the photoinitiator is reacted using blue light (420-500 nm). In some embodiments, the photoinitiator is reacted using IR light (800-2500 nm). Light output can be adjusted to control crosslinking and / or polymerization reactions. The polymerization can be controlled to control the properties and / or properties of the formed hydrogel.

In some embodiments, the particle may be or include an inorganic polymer such as silica (SiO ₂ ). In some embodiments, the particles according to the invention are based on silica. For example, silicate materials are useful for applying the present invention because of their biocompatibility, ease of manufacture and functionalization, and high surface-to-volume ratios. Silica-based particles such as porous silica particles and any modified or hybrid particles can be used in accordance with the present invention.

As is well known in the art, silica-based particles can be prepared in a variety of ways. Some methods apply Stober synthesis involving the hydrolysis of, or modification of, tetraethoxyorthosilicate (TEOS) catalyzed by ammonia in a water / ethanol mixture. In some embodiments, silica-based particles are synthesized using known sol-gel chemistry, for example by hydrolysis of the silica precursor or precursors. Silica precursors are provided as a silica precursor and / or silica precursor derivative solution. Hydrolysis is carried out in alkaline (basic) or acidic conditions. For example, hydrolysis is performed by adding ammonium hydroxide to a solution containing one or more silica precursors and / or derivatives. Silica precursors are compounds that can form silica under hydrolysis conditions. Exemplary silica precursors include, but are not limited to, organosilanes such as tetraethoxysilane (TEOS), tetramethoxysilane (TMOS), and the like. In some embodiments, the silica precursor has a functional group. Examples of such silica precursors include, but are not limited to, isocyanatopropyltriethoxysilane (ICPTS), aminopropyltrimethoxysilane (APTS), mercaptopropyltrimethoxysilane (MPTS), and the like. Include. In some embodiments, a microemulsion method is applied to synthesize particles suitable for use in the present invention. For example, water-in-oil emulsions, in which water droplets are dispersed in a continuous medium of oil and surfactant in nano-sized liquids, acting as nano reactors for nanoparticle synthesis, provide a convenient method.

In some embodiments, the particles have detectable materials that generate fluorescence, luminescence and / or scattering signals. In certain embodiments, the particles have quantum dots (QD). QDs are bright, fluorescent nanocrystals that are physically small enough to give inherent optical and electronic properties with quantum confinement effects. Semiconductor QDs sometimes consist of group II-VI or III-V atoms in the periodic table, but other components are possible. By varying the size and composition, the emission wavelength can be adjusted from blue to near infrared ( ie , adjusted in a predictable and controllable manner). QDs generally have a broad absorption spectrum and a narrow emission spectrum. Thus different QDs having optical characteristics ( eg , peak emission wavelength) that can be distinguished using a single source can be excited. In general, QDs are brighter and have more light stability than most conventional fluorescent dyes. QD and synthetic methods are well known in the art (see, eg , US Pat. Nos. 6,322,901; 6,576,291; and 6,815,064; these are incorporated herein by reference). A variety of different materials can be applied to make the QD water soluble (see, eg , US Pat. Nos. 6,423,551; 6,251,303; 6,319,426; 6,426,513; 6,444,143; and 6,649,138; all of which are incorporated herein by reference). For example, QD can be dissolved using amphiphilic polymers. Exemplary polymers are applicable oxyl amine-derivatized phospholipids include those of, polyanhydrides, block copolymers, and so-modified low-molecular weight polyacrylic acid, polyethylene-glycol (PEG).

Exemplary QDs suitable for use in accordance with the present invention in some embodiments are those that are commercially available with a wide variety of absorption and emission spectra, for example , Quantum Dot Corp. (Hayward CA; now owned by Invitrogen) or from Evident Technologies (Troy, NY). For example, QDs with peak emission wavelengths of about 525 nm, about 535 nm, about 545 nm, about 565 nm, about 585 nm, about 605 nm, about 655 nm, about 705 nm, and about 800 nm can be used. have. Thus, the QD may be exceeded in some cases but may have color gamuts spanning the visible spectral region.

In certain embodiments, optically detectable particles are or include metal particles. Metals used include, but are not limited to, gold, silver, iron, cobalt, zinc, cadmium, nickel, gadolinium, chromium, copper, manganese, palladium, tin, and alloys thereof. Any of these metal oxides can also be applied.

Certain metal particles called plasmon resonance particles exhibit well known plasmon resonance. Plasmon resonance particle spectral features ( eg , peak wavelength) depend on many factors, including particle material composition, particle shape and size, refractive index or dielectric properties of the surrounding medium, and the presence or absence of surrounding other particles. Depending on the particular particle shape, size and composition selection, particles can be produced with distinguishable optically detectable properties of the width, thus allowing simultaneous detection of multiple samples using particles with different properties such as peak scattering wavelengths. Can be.

Magnetic properties of the particles can be used in accordance with the present invention. In some embodiments the particles are or comprise magnetic particles, ie magnetically reactive particles containing one or more metals or oxides or hydroxides thereof. Magnetic particles include one or more ferromagnetic, ferromagnetic, paramagnetic, and / or superparamagnetic materials. Useful particles are: iron, cobalt, nickel, niobium, magnetic iron oxide, hydroxides such as magnetite (γ-Fe ₂ O ₃ ), magnetite (Fe ₃ O ₄ ), feroxyhyte (FeO (OH)) , 2- or 3-valent iron and 2- or 3-valent other metal ions such as Co (II), Mn (II), Cu (II), Ni (II), Cr (III), Gd (III ), Wholly or partially in one or more materials selected from complex or hydroxides of monothermal transition metal ions such as Dy (III), Sm (III), mixtures of the oxides or hydroxides, and mixtures of any of the above components Are manufactured. See, for a suitable synthesis method of these predetermined particles See, eg , US Pat. No. 5,916,539, incorporated herein by reference. Additional materials that can be used in magnetic particles include yttrium, europium, and vanadium.

Size and shape

In general, particles suitable for the present invention may have any size. In some embodiments, suitable particles have a maximum dimension ( eg diameter) of 1000 micrometers (um). In some embodiments, suitable particles have a maximum dimension of 500 um or less. In some embodiments, suitable particles have a maximum dimension of about 250 um or less. In some embodiments, suitable particles have a maximum dimension ( eg diameter) of about 200 um, about 150 um, about 100 um, about 90 um, about 80 um, about 70 um, about 60 um, about 50 um, About 40 um, about 30 um, about 20 um, or about 10 um or less. In some embodiments, suitable particles have a maximum dimension of 1000 nm or less. In some embodiments, suitable particles have a maximum dimension of 500 nm or less. In some embodiments, suitable particles have a maximum dimension of about 250 nm or less. In some embodiments, the maximum dimension is hydrodynamic diameter.

Suitable particles are of various forms and include, but are not limited to, spherical, spherical, cylindrical, oval, oval, shell, cube, rectangular, conical, pyramidal, rod-shaped ( eg, cylinders with square or rectangular cross sections). Or elongated structures), tetrapods (particles with four leg-like appendages), triangles, prisms, and the like. In some embodiments, the particles are rod-shaped. In some embodiments, the particles are rod-shaped. In some embodiments, the particles are in bead-shaped. In some embodiments, the particles are pillar-shaped. In some embodiments, the particles are in a form similar to a ribbon or chain. In some embodiments, the particles can be of any geometry or symmetry. For example, planar, circular, annular, round, tubular, ring-shaped, tetrahedral, hexagonal, octagonal particles, particles of other regular geometry, and / or irregular geometric particles may be used in the present invention. Additional suitable particles of various sizes and shapes are disclosed in US Pat. No. 7,709,544 and US Pat. No. 7,947,487 and used in the present invention, which are incorporated herein by reference.

The particles can have various aspect ratios of these dimensions such as length / width, length / thickness, etc. The particles may, in some embodiments, have at least one dimension, such as length, greater than another dimension, such as width. In accordance with the present invention, particles having at least one aspect ratio of one or more are particularly useful for fluid flow scanning ( eg , in flow cytometers) by promoting self-alignment. In some embodiments, the particles have at least one aspect ratio of at least 1.5: 1, at least 2: 1, at least 2.5: 1, at least 3: 1, at least 5: 1, at least 10: 1, at least 15: 1, or more. Have

It is desirable to use a relatively uniform population of particles in size, shape, and / or composition so that each particle has similar properties. In some embodiments, a population of particles with uniform diameters (eg, hydrodynamic diameters) is used. As used herein, a population of particles with uniform diameters (eg, hydrodynamic diameters) means a diameter (eg, within 5%, 10%, or 20% of an average diameter (eg, hydrodynamic diameter)). For example, a population of particles having a hydrodynamic diameter) is at least about 80%, at least about 90%, or at least about 95%. In some embodiments, the average diameter (eg, hydrodynamic diameter) of particles having uniform diameters (eg, hydrodynamic diameters) is in the range described above. In some embodiments, particles having uniform diameters (eg, hydrodynamic diameters) refer to a population of particles having a polydispersity index of 0.2, 0.1, 0.05, 0.01, or 0.005 or less. For example, the polydispersity index of the particles used in accordance with the present invention is about 0.005 to about 0.1. Without wishing to be bound by any theory, homogeneous particles (eg, in particle size) have higher repeatability and higher accuracy herein. In some embodiments, the population of particles can be heterogeneous in size, shape, and / or composition.

The particles can be solid or hollow and can include one or more layers ( eg, nanocells , nanorings, etc. ). The particles can have a core / cell structure, where the core (s) and cell (s) can be made of different materials. The particles may comprise gradient or homogeneous alloys. The particles may be composite particles made of two or more materials, one, one or more, or all of the materials having magnetic properties, electrically detectable properties, and / or optically detectable properties.

The particles can have a coating layer. For example , if the particles contain cytotoxic materials, it is advantageous to use a biocompatible coating layer. Suitable coating materials include but are not limited to natural proteins such as bovine serum albumin (BSA), biocompatible hydrophilic polymers such as polyethylene glycol (PEG) or PEG derivatives, phospholipid- (PEG), silica, lipids, polymers include those, for example, the carbohydrate dextran, the other inventive nanoparticles that can be associated with the nanoparticles, and so on. The coating is applied or assembled in various ways by dipping, using the layer-by-layer technique, self-assembly, conjugation, and the like . Self-assembly refers to the spontaneous assembly process of higher order structures according to the mutual natural attraction of higher order structural ( eg molecules) components. This typically occurs through random movement and bond formation of molecules based on size, shape, composition, or chemical properties. In some embodiments, the coated particles are also referred to as functionalized particles or surface treated particles.

In certain embodiments of the invention, the particle is porous, meaning that the particle has generally small pores or channels relative to the particle size. For example, the particles can be porous silica particles, such as porous silica nanoparticles or have a porous silica coating. The particles have pores of about 1 nm to about 200 nm in diameter, for example about 1 nm to 50 nm in diameter. About 10% to 95% of the particle volume is pores inside the pores or channels.

In some embodiments, the particles optionally include one or more dispersion media, surfactants, sustained release agents, or other pharmaceutically acceptable excipients. In some embodiments, the particles optionally include one or more plasticizers or additives.

In various embodiments, the particles described herein have at least one region with one or more probes described herein. In some embodiments, the particles have at least one coding region. In some embodiments, the particles have at least one region with at least one coding region and one or more probes. Such regions may be discrete regions of substrates (subjects) containing particles applied according to the invention. In some embodiments, each region is optionally functionalized. In various embodiments, the particles described herein can have an orientation indicator (eg, the coding region first followed by the probe region or vice versa).

Functionalization

Known in the art (eg, described in US Pat. No. 7,709,544 and US Pat. No. 7,947,487) and the various methods provided herein are useful for the functionalization of the substrates or subjects (eg, particles) described herein. .

Various functional materials or groups can be introduced to the substrate surfaces that provide for selective functionalization (eg, capture of coding adapters, probes or target nucleic acids). Such functional materials may be chemically attached to the surface, for example covalently, or physically attached or enclosed therein.

In some embodiments, at least a portion of the substrate is made of monomers. Such monomers provide for selective functionalization in a substrate formed alone or in combination with copolymerized species. For example, the functional material may be provided as a monomer or as part of a monomer that is polymerized, for example, by an etch-polymerization step of particle synthesis (see US Pat. No. 7,709,544 and US Pat. No. 7,947,487).

The invention is not limited to any particular encoding method. The coded representation can be a visible detectable feature, such as color, apparent size, or visibility ( ie, simply whether a particle is visible in certain conditions).

In various embodiments, graphical representations and / or optically detectable representations are particularly useful in the present invention. In various embodiments of the present invention, the schematic coding discussed in US Pat. No. 7,947,487 and the coding disclosed herein (eg, general purpose coding) apply.

In some embodiments, the graphical representation for encoding is or includes one or more spatial pattern features. In some embodiments, the spatial pattern feature includes a number of open and closed coding elements. The coding elements are arranged in a two-dimensional grid. The coding elements also have non-uniform shapes or sizes. In certain embodiments, the spatial pattern feature further includes an orientation indicator.

Additionally or alternatively, optical indications can be applied according to the invention. In some embodiments, the optical representation for encoding is or includes a feature of absorption, emission, reflection, refraction, interference, diffraction, dispersion, scattering, or any combination thereof.

In some embodiments, the optical indication is inherent in the functional substrates according to the present invention. In some embodiments, an optical indication is introduced to the functionalizing substrates. Such introduction is possible before, concurrently and after contact with the sample, with which a signal is generated and / or such a signal is detected.

By way of example only, the functionalizing substrate has no functional substance per se, but has a functional substance that can be detected by further action with and / or modification by another substance. In some embodiments, such functional material may be a functional group or moiety that promotes binding to a substrate and other entities.

Thus, in contrast to the more or, the substrate surface is functionalized with the substrate and other objects are introduced chemically functional materials to promote bonding with (for example, the probe field coded preparation, and so on). Suitable functional materials are introduced covalently to the substrate surfaces. In some embodiments, coupling agents are used with various substrates for functionalization. Exemplary coupling agents include difunctional, trifunctional, higher functional coupling agents, which are well known in the art, such as MeSiCl ₃ , dioctylphthalate, polyethylene-glycol (PEG), and the like. In some embodiments, the substrates are functionalized by covalently attaching streptavidin to the surface with a heterobifunctional crosslinker having a polyethylene-glycol (PEG) spacer arm. Various functionalization methods are known in the art and may be used to implement the present invention.

In some embodiments, the substrate surface is functionalized by introducing capture or anchor oligonucleotides to facilitate the capture and immobilization of individual nucleic acid molecules, encoding adapters or probes, such as single-stranded polynucleotide templates. In some embodiments, the capture or anchor oligonucleotides have sequences that are complementary to the universal sequence present in the nucleic acid template molecules. Exemplary capture or anchor oligonucleotides have varying numbers of nucleotides. For example, suitable oligonucleotides are 1-50 nucleotides (e.g., 3-40, 3-30, 3-20, 30-15, 3-10, 6-40, 6-30, 6-20 , 6-10, 8-30, 8-20, 8-15, 10-30, 10-20, 10-15 nucleotides). In some embodiments, suitable oligonucleotides have 1, 2, 3, 6, 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45, or 50 nucleotides. Various methods for designing and synthesizing suitable capture or anchor oligonucleotides are known in the art and these methods are implemented by one of ordinary skill in the art.

In some embodiments, capture or anchor oligonucleotides are described, for example, in Lund et al. Nucleic Adds Research, 16: 10861-10880 (1988); Albretsen et al, Anal. Biochem., 189: 40-50 (1990); Wolf et al, Nucleic Acids Research, 15: 2911-2926 (1987); Or synthesized individually and attached to the substrate surface, as disclosed by Ghosh et al, Nucleic Acids Research, 15: 5353-5372 (1987).

In some embodiments, the bond is covalent. In still other embodiments, the covalent linkage of the capture or anchor oligonucleotides and the nucleic acid template (s) to the substrate may be a crosslinker such as l-ethyl-3- (3-dimethylaminopropyl) -carbodiimide hydrochloride (EDC ), Succinic anhydride, phenyldiisothiocyanate or maleic anhydride, or hetero-bifunctional crosslinkers such as m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS), N-succinimidyl [4 Iodoacetyl] aminobenzoate (SIAB), succinimidyl 4- [N-maleimidomethyl] cyclohexane-1-carboxylate (SMCC), Ny-maleimidobutyryloxy-succinimide ester (GMBS ), Succinimidyl-4- [p-maleimidophenyl] butyrate (SMPB) and the corresponding sulfo (water soluble) compounds.

In some embodiments, a functional substrate having chemical groups or capture or anchor oligonucleotides is used for general purpose coding and / or probe region functionalization.

Universal Coding

General purpose coding allows the production of functionalized substrates in a general purpose structure, which results in substrate subgroups with distinct barcodes that are more coded and show distinct identity. In the case of highly multiplexed identification, this approach saves manufacturing time and cost compared to synthesizing a subpopulation of substrates independently for each target.

In some embodiments, the functionalization substrate includes one or more general purpose coding regions. These coding regions are spaced by inactive or non-functionalization regions. Typically, each universal coding region has one or more templates for capturing encoding adapters by covalent linkages through functional groups or by hybridization and / or ligase reaction with capture or anchor oligonucleotides on the functionalized surface. In some embodiments, the template is or comprises a single-stranded polynucleotide. For example, such single-stranded polynucleotides comprise predetermined nucleotide sequences that specifically bind to the desired coding adapter. In some embodiments, the template further comprises a stem-loop structure (ie, a hairpin structure). Predetermined nucleotide sequences, in certain embodiments, promote ligase reactions with template and coding adapters adjacent to stem-loop structures. In such embodiments, the coded adapter that engages the template typically does not form a secondary structure. In some embodiments, the single stranded template does not form a hairpin structure, such as an encoded adapter.

In general, predetermined nucleotide sequences having any base combinations or lengths may be used in accordance with the present invention. In some embodiments, the predetermined nucleotide sequence is 1, 2, 3 bases or more in length. In some embodiments, the length of the predetermined nucleotide sequence is 4 bases, 5 bases, 6 bases, 7 bases, 8 bases, 9 bases, 10 bases, 11 bases, 12 bases, 13 bases. , 14 bases, 15 bases, 20 bases, 25 bases or 30 bases or more. In some embodiments, the length of a predetermined nucleotide sequence is in the range between any two of the above values. The length of the predetermined nucleotide sequences may be the same or different for one substrate.

In some embodiments, single-stranded polynucleotide templates can be used to capture coding adapters. Suitable encoding adapters are DNA, RNA, or any type of nucleic acid analog. In various embodiments, the encoding adapter is or comprises a single-stranded polynucleotide. In some embodiments, the encoding adapter comprises a nucleotide sequence that is complementary to the predetermined sequence of the template. Typically, the coding adapter has 30, 25, 20, 18, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotides.

In some embodiments, the encoding adapters, once linked with the template, are coupled with the template by T4 DNA ligase or other enzyme or chemical coupling.

Coded adapters may or may not be labeled. In some embodiments, the coding adapters are labeled with a detectable material (eg, optically detectable material). Various detectable materials can be used and include phosphors, chromophores, radioisotopes, quantum dots, nanoparticles and / or insert DNA / RNA dyes. Further examples of detectable materials are described in the Detectable Materials section above.

In various embodiments, the coded adapters used in accordance with the present invention are a mixture of label and unlabeled coded adapters. In some embodiments, labeled and unlabeled encoding adapters have identical or similar sequences and bind to the same templates. In some embodiments, the labeled coded adapters to the unlabeled coded adapter content can be varied to adjust the amount of signal (eg fluorescence) generated in the region to a desired level. In some embodiments, a lock sequence can be used to selectively indicate which adapters are coupled and connected to each hairpin probe region. In this way, various strips of independently assignable hairpin probe regions are used for coding.

In some embodiments, at least one label encoded adapter signal is used to determine the orientation of the substrate. In some embodiments, at least one marker coded adapter signal is used to normalize detectable signals of other label coded adapters.

Multiple colors (or generically emission wavelengths) can be used when implementing the general purpose coding method described herein. This is achieved using a blend of general purpose adapters modified with various species, such as phosphors with inherent emission spectra. Depending on the respective adapter content added to the ligase mix, a variable content can be linked to the templates embedded in the particles, so that the level of multiple "colors" in each coding region can be adjusted. In one embodiment, two phosphors are used in the particles / substrates to generate two-color codes as follows, but more colors can be readily applied.

In some embodiments, the fluorescence in each coding region is at various levels, for example up to 10-20 levels (eg, 1, 2, 3, 4, 5, 6, 7, 8, 9, Up to 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 levels). For example, if three coding regions are used and each of the 10 levels is separated, 1000 (10 × 10 × 10) unique codes are possible. Additionally or alternatively, multiple signals (eg different fluorescent colors) can be used for encoding. In some embodiments, each coding region has one signal that is distinct from one another. In some embodiments, substrates and coding adapters are designed such that at least one coding region of the substrates is attached with one or more types of coding adapters that generate multiple signals. In some embodiments, each coding region has multiple signals and adjusts the coding adapters content to achieve coding at the desired signal ratio.

Probe Area Functionalization

The substrate used by the present invention includes one or more probe-bearing regions in addition to the coding regions. Two typical methods for general purpose coding and probe functionalization are shown in FIGS. 1 and 2 .

In some embodiments, each probe region has anchors for attaching probes of interest according to, for example, a ligation-based method. The ligase reaction is carried out in three species (anchors, linkers, and probes) or in two species (hairpin anchors and probes). A probe-region functionalization method employing a 3-species ligase reaction, a 2-species ligase reaction, and a chemical modification is shown in FIG. 3 .

In some embodiments, probe region functionalization includes chemical modifications, such as peptide bonds, that attach the amination probes to the carboxylated substrates by the carbodiimide method. Detailed example methods for functionalization are shown in the Examples section below.

Various methods known in the art design the desired probes specific for the target nucleic acids. In some embodiments, the desired probes for probe region functionalization include nucleic acid probes for post-hybrid labeling as described herein.

In some embodiments, the probe regions and the coding regions are spaced apart from each other by inactive regions. In some embodiments, one or more probe-bearing regions and one or more coding regions overlap each other. In some embodiments, the region having the coding and the probe may be the same region.

In some embodiments, different detectable signals (eg, different fluorescent colors) are used for the coding regions and the probe-bearing regions. In some embodiments, in particular, the same type of detectable signals are applied when the coding regions and the probe-containing regions are spaced apart from each other.

In two-piece functionalization, adapters with linear anchors and hairpins can be used. Adapter and anchor species are designed to minimize hairpin formation or tightly bound hairpins under ligase conditions. Detectable materials for encoding include phosphors, chromophores, radioactive species, magnetic species, quantum dots, conductive materials, and the like. Any number of coding regions are used, and they do not need to consist of strips. Each coded region may include any number of colors or other distinctive signals. These methods can also be applied to other substrates, including beads, flat surfaces, gel pads, and the like. Substrates can be solids, polymers, emulsions, and the like.

In addition to ligase reaction based methods, the present methods for general purpose coding and / or functionalization can be implemented with other enzymes including, among others, ligases, polymerases. For example, T4 DNA ligase is used in the following experiments, but other enzymes that bind oligonucleotides to each other can be used. Other enzymes include, but are not limited to, other DNA ligases, RNA ligases, polymerases, and the like. Alternatively, polymerases can also be used to stretch the oligonucleotides using the desired nucleic acid template by means of additional nucleic acid probes for functionalized or labeled species for encoding or detection ( FIG. 4 ). Applying this method or a ligase-based method, multiple probe regions are added to a single particle when multiple probe “anchors” are used.

Target nucleic acids

The methods and compositions described herein are applied to detect any nucleic acids. In general, the target nucleic acids are DNA, RNA forms, or any combination thereof. In certain embodiments of the invention, the target nucleic acid may be or include a gene, regulatory sequence, genomic DNA, cDNA, mRNA, rRNA, RNA, including microRNA, or any combination thereof.

Target nucleic acids are, in various embodiments, for example those found in biological organisms, including microorganisms or infectious agents, or any naturally occurring, genetically engineered or synthesized component thereof.

In accordance with the present invention, provided compositions and methods are particularly useful for quantifying transcription (eg, primary transcripts, mRNA, etc.) nucleic acids. In some embodiments, the methods provided herein are used to detect and / or quantify miRNAs. miRNAs are found in the genomes of humans, animals, plants and viruses. In accordance with the present invention, the target nucleic acid, in some embodiments, is or comprises one or more miRNAs generated from endogenous hairpin-form transcripts. In some embodiments, the target nucleic acid is or includes one or more miRNAs transcribed as long primary transcripts (pri-microRNAs), for example, by RNA polymerase II in an animal. The miRNA database ( http://microrna.sanger.ac.uk/sequences/ftp.shtml ) currently lists a total of 1424 human miRNA genes, representing nearly 3% of protein-encoding genes. Many miRNAs are considered important for controlling gene expression. Typically, microRNAs are produced in precursor form and typically proceed to mature form by cleaving the 3 'arm of the precursor stem-loop structure. Thus, precursor microRNA and mature microRNA have the same 5 'end but the 3' end is distinct. Selective end-labeling can be applied to detect mature microRNA species without designating a capture sequence complementary to the 3 'end sequence to detect precursor species. Examples of selective end-labeling are described in the Examples section.

Any of a variety of biological samples are suitable for applying the methods described herein. In general, any biological samples containing nucleic acids (eg, cells, tissues, etc.) may be used. Biological sample types include, but are not limited to, cells, tissue, whole blood, plasma, serum, urine, feces, saliva, umbilical cord blood, chorionic villus amniotic fluid samples, and cervical lavage fluid. Any type of tissue biopsy may be used. G. In cell culture of any of the above biological samples such as chorionic villus culture, positive and / or positive cell culture medium, blood culture medium (e.g., a lymphocyte culture), and so on also can be used by methods of the present invention . In some embodiments, biological samples include diseased cells, such as cancer or tumor cells.

Thus, typical biological samples suitable in the present invention include heterogeneous nucleic acids. In some embodiments, the biological sample comprises a mixture of nucleic acids obtained from different types of cells (eg, normal cells and disease cells such as tumor cells). In some embodiments, the biological sample (eg, blood, serum or plasma) comprises a mixture of maternal nucleic acids and fetal nucleic acids.

In some embodiments, the present invention is used to detect target nucleic acids present in low abundance or in rare phenomena in a biological sample. In some embodiments, target nucleus detectable by the method of the present invention is present at a concentration in the range of 0.1 amol-10,000 amol. In some embodiments, the target nucleic acid concentration is at most 10,000 amol, at most 5,000 amol, at most 1,000 amol, at most 800 amol, at most 600 amol, at most 400 amol, at most 200 amol, at most 100 amol, at most 50 amol, at most 40 amol, Up to 30 amol, up to 20 amol, up to 10 amol, or up to 1 amol. In some embodiments, the target nucleic acid content detected by the method of the invention is 1% or less (eg, 0.5%, 0.1%, 0.01%, 0.001%, 0.0001% or less) of total nucleic acids in a biological sample. In some embodiments, the target nucleic acid content detected by the method of the invention is 1% or less (eg, 0.5%, 0.1%, 0.01%, 0.001%, 0.0001% or less) of total nucleic acids in a biological sample. In some embodiments, the target nucleic acid content detected by the method of the present invention is no more than one millionth of the total nucleic acids in the biological sample. In some embodiments, the target nucleic acid content detected by the method of the present invention is less than one tenth of the total nucleic acids in the biological sample. The target nucleic acid can be detected in the crude sample or as an isolated or purified sample.

Scanning and Quantification

The substrate or subject described herein can be characterized using a variety of methods. In particular, various methods using fluid flow scanning and / or static imaging can detect the substrate bound to the target nucleic acid and / or determine the target nucleic acid content. Typically, the target nucleic acid attached to the substrates is determined by detecting signals. In accordance with the present invention, signals that “mark” the target nucleic acid are generally associated with the identification of the substrate to which the target nucleic acid is attached or the location on the substrate. For example, signals are generated from one or more detectably labeled probes or targets associated with signals indicating one or more encoded regions of a substrate having probes or targets.

In some embodiments, the signals indicative of the target nucleic acids are generally distinguished from the signals indicative of the identification of the substrate. In some embodiments, probes specific to target nucleic acids or universal adapters and encoding adapters for encoding regions are labeled with distinct detectable signals. For example, probes or universal adapters specific for the target nucleic acid are labeled with a phosphor having a different emission spectrum ( ie , color and wavelength) than that of the fluorescent labeled region. Thus, in some embodiments, a substrate (eg, particles) of the present invention may be scanned using a multi-scanning system involving one or more excitation sources and detectors (see FIG. 5 ) . Can be.

In some embodiments, monochrome scanning is applied. Signals representing separate “code” and “probe” regions are used to identify substrates (eg, particles) and to capture targets, respectively. By way of example, using the particles described in detail below, signal patterns from the coding regions (eg, bearing holes, bands, coding adapters and / or combinations thereof) of the particle may be probed at a particular particle. It forms the basis of the schematic multiple barcodes for identifying (s). In some embodiments, unlike conventional bead-based systems using optical coding of spheres, monochromatic scanning is possible due to the structure in which the particles have a plurality of discrete regions, and only one excitation source and one detector are required. . In some embodiments, particles may have schematic features (eg, bands, holes, or the like) having various fluorescence intensities (one or more wavelengths), optical properties, dimensions, and the like. (Reference figure 6 ).

Particles are used by way of example to show the scanning and quantification process which is described in more detail below. However, the methods described herein may be applied to various other types of substrates or subjects.

Particles investigation

In some embodiments, the present invention provides a method of characterizing multiple functional objects (eg, particles), wherein (a) each has one or more irradiated areas that can be detected as a series of events. Irradiating a plurality of objects (eg, particles); (b) recording a number of phenomena corresponding to each irradiated area where each phenomena can be detected above a predetermined trigger threshold; (c) categorizing the plurality of phenomena, and (d) characterizing the plurality of objects according to the categorized phenomena.

In some embodiments, particles are irradiated using image analysis in a static or fluid flow setting. For high throughput applications, it is desirable to quickly scan the particles, preferably using existing commercial equipment. For example, flow cytometers that provide particle alignment, precise illumination, and accurate fluorescence emission quantification are particularly useful for fluid flow analysis of fluorescently labeled beads and particles. In some embodiments, encoded multi-functional particles are designed that can be scanned using a commercially available or custom-designed fluid flow mechanism, such as a flow cytometer.

In some embodiments, particles suitable for fluid flow scanning are produced by mimicking a series of cells (eg, 2, 3, 4, 5, or more) that flow through an irradiation zone. In certain embodiments, the outer regions (eg, terminal both regions) of suitable particles are coding regions, and one or more inner regions have probes to which the target is captured. Each of the coding region and the probe region are individually examined (eg, sequentially or non-simultaneously) and each region is also referred to as an irradiation region. In certain embodiments, rod-shaped particles having multiple irradiation areas are recorded "phenomena" using standard cytometry signal processing. By analyzing the order and time-proximity of these phenomena, one can infer which belongs to the same particle. These phenomena are then analyzed to decode the particles and quantify the target bound to the probe area. Signal quantification is achieved using fluorescence, light scattering, luminescence, and the like.

Typically, raw signals are obtained at the cytometer detector (or signal processing board) using standard cytometry software. Signals are then processed using custom software to import standard flow cytometry (FCS) files and reconstruct the phenomena into particles and corresponding probes and coding regions.

Various flow cytometers and other fluid flow reading instruments may be used by the present invention, and various commercially available flow cytometers and custom design instruments are included. Exemplary suitable flow cytometers include, but are not limited to, Millipore Guava 8HT, Guava 5HT, Accuri C6, BD FACSCalibur.

Multi-Phenomena Particles

As a non-limiting example, when a particle travels through the flow cell of the cytometer, the particle is excited to an illumination point and detectors are used to monitor various parameters including forward and lateral scattering of illumination, and various emission wavelengths. . By setting a threshold for one of these parameters in the trigger channel, the user can define the cases in which the cytometer software records as events. If the detector signal in the trigger channel exceeds the threshold level set by the user, the cytometry hardware and software begin recording the phenomenon and measure the maximum signal magnitude and integral area from each detector when the trigger signal remains above the threshold. . Typically the phenomena are reported with the height and area observed in each channel along with the development width and time-stamp when the phenomenon occurs.

Typically, single particles or beads are recorded as a single phenomenon. However, in various embodiments, particles having multiple functional regions (eg, rod-shaped particles) according to the present invention are read out as a series of distinct phenomena. This is accomplished using particles having functional regions (eg fluorescence) spaced by inactive regions (eg non-fluorescence). If the threshold-triggered individuals are included in the functional areas of the particles but not in the inactive areas, a typical cytometry signal processing software records the functional areas as discrete phenomena. This can be accomplished using individuals that cause scattering or fluorescence. Such entities include microparticles, nanoparticles, reflective monomers, metallic materials, fluorescently-labeled monomers, quantum dots, fluorescent dyes, carbon nanotubes, liquid crystals, and various detectable entities described herein. Include.

In the Examples section, examples are provided that demonstrate this manner of operation and differentiation from standard cell assays (Example 9). Particle scanning examples using specific flow cytometry are provided in Example 10.

Data Analysis

For data analysis, we create algorithms that classify phenomena into particles, orient particles to normalize fluorescence against a standard if necessary, and quantify fluorescence, scattering, or development width in each code and probe region. . The confidence level is then given to the code for each particle, and those that are not called with the intended confidence level are excluded from the analysis. The fluorescence in the probe area is then used to determine the target content present in the assay sample. Such a system can be easily automated using software that has performed the scanning process or subsequent analysis.

Classification of phenomena

In some embodiments, phenomena are classified based on spatiotemporal proximity. In some embodiments, phenomena are classified based on the patterns of characteristics measured for each phenomena.

Typically, each phenomenon recorded by the cytometer is given a time stamp, for example, with a predetermined resolution of 1 ms, based on the flow rate in each cell assay. For example, particles typically move the flow cell at a rate of ˜1 m / s, so the time to irradiate particles of 200 ° length lasts ˜0.2 ms. Thus, it is expected that two phenomena recorded in a single multi functional particle appear in the same time stamp.

In some embodiments, correction beads are scanned at random in the data acquisition process. Typically, at least one phenomenon is recorded for the calibration beads. Multifunctional particles, however, typically exhibit a group of two or four phenomena per time stamp, which fits well with the theory that each particle is read into two phenomena. It is also clearly seen that there is a high and low level of fluorescence reading in each time stamping process from the development versus time plot. The particles were designed to have one bright and one faint fluorescence region in the FL-2 channel, which also supports the theory that each particle is read out with two discrete phenomena. This approach can also be applied to more than three T phenomena per particle. Each region / phenomena is variable in fluorescence level, forward or lateral scattering, and width.

It is possible to include discrete levels of multiple phosphors in the code region of each of the multifunctional particles. As a technical verification, rod-shaped particles, 200 × 35 × 30 mm, with a single 60 mm coding area at one end were used. The encoded region was labeled using four distinct levels of Cy3 and Cy5 fluorescent dyes. Particles were analyzed with an Accuri C6 cytometer at a flow rate of 100 ml / min, core size of 40 mm, and a threshold of 5000 at FL4. The results are shown in FIG.

The diagram of FIG. 7 shows that distinct fluorescent fingerprints can be generated in the coding region of each of the multifunctional particles. Each group of data points represents a separate code.

Raw signal reading

In some embodiments, investigating multi-functional particles in standard flow cytometers is to obtain a signal from a cytometer detector, which is then processed into phenomena with the instrument's firmware and custom software to ensure particle scan identification, orientation, and analysis. Is done.

In some embodiments, the raw data files generated by the scanning process ( eg , 20 million dots / scan) are separated for separate particle markings, code identification indicated by each particle, and binding target content quantification. Designed and analyzed by a custom written MATLAB algorithm. The algorithm processed a scan of 50-ul samples in 5 s, and the method is suitable for high efficiency applications. In the first filter step, the algorithm extracts scan portions that exceed the threshold voltage and examines whether each feature is identified by the particle representation for the extraction zone. Using fluorescence code region specific properties as reference points, an estimate for each particle velocity with high-reliability is determined and utilized to pinpoint trough positions for five code holes. Particle orientation ( ie , probe- or cord-first) was set using fixed-value “3” holes bounded by inert buffer regions. After the initial code identification is calculated from the bone depth, the bone depth standard deviation of the designated holes at the same level is measured and secondary reviewed and corrected if necessary. In the final decoding step, the confidence score for the particle is calculated by calculating the correlation linearity between bone depth and allocation level. If the Pearson coefficient is 0.97 or less, particle decoding is rejected.

In order to calculate the binding target content, the measured particle velocity is used to infer the probe region center position. For simplicity, a search box is used to examine the scan in this area and search to identify local maximums that can be correlated with the target-binding phenomenon. If a maximum is found, the search window position along the scan profile is adjusted until the two endpoints are sufficiently closed at the signal amplitude, so that the nearly symmetric maximum portion that is averaged for quantification purposes is selected. If no maximum is found, the mean signal is calculated using the original estimate for the probe center without a search box. To calculate the background for a given probe sequence and culture conditions, for example, the same synthetic portions of particles are cultured in the presence of only 100 amol of miSpike target by the above procedure. The method provides probe-dependent background measurements derived from the PEG support and universal adapters used in the labeling process. In addition, in all code identification and target level calculations, particles are considered if the target level is greater than the 3/4 quartile upper or quartile lower 1 quartile range of the data set consisting of target levels associated with the probe. It doesn't work.

Various embodiments for particle scanning and quantification are provided in the Examples section. Additional scanning and quantification methods are described in the same international application name "Scanning Multi Functional Particles", which is incorporated herein in its entirety.

Etc Examples

There are several variations and alternatives to the above embodiments. Although rod-shaped particles are used in the above embodiments, the present invention can be applied to scan objects or particles having many other shapes as well. For example, particles may be anisotropic, have a head on one side, include round shapes, have holes, and the like. In some embodiments, the invention is directed to scanning a variety of multi-functional entities including long nucleic acids, DNA chainfolds, self-assembled structures, biological organisms, string-like objects, ribbon-like objects, etc. Can be applied. In addition, any combination of information, including height, area, width, or any combination thereof, recorded by the cytometer for each phenomenon can be used for encoding or target quantification.

Other commercially available devices can read particles with multiple functional regions and are used to implement the present invention. One example is a device that can measure the electrical conductivity, or electrical resistance change, of a fluid channel such as a coulter counter. The current or voltage generated by the particles by the detectors of these systems can be used to characterize particle size, morphology, chemical composition, or surface properties. In addition, a laser-scanning cytometer (LSC) that provides high resolution visualization of the flowing particles can be used to identify probe areas and identification areas of particles having several functionalized areas. Such LSC systems are commercially available, for example from the company CompuCyte. There are also commercial cytometers (eg Amnis ImageStream) that image when cells / particles pass. They are used with suitable image-processing software to decode the particles and quantify the target. It is also possible to use non-fluorescence quantification means such as surface-plasmon resonance or radiation.

apply

The present invention applies to many fields, including but not limited to, the diagnosis and prognosis of diseases, diseases or conditions based on the detection or quantification of a target nucleic acid (eg, microRNA, DNA or mRNA) in a biological sample. do.

Those skilled in the art, having read the present invention, will appreciate their broad application. For example, the invention is not limited to cancer (eg, lung cancer, breast cancer, gastric cancer, pancreatic cancer, lymphoma, leukemia, colon cancer, liver cancer, etc.), diabetes, degenerative neurological diseases (eg, Alzheimer's), infectious diseases, genetic diseases can be applied to diagnose or predict a number of diseases.

Representative bacterial infectious agents that may be detected and / or determined by the present invention include, but are not limited to, E. coli, Salmonella, Shigella, Klebsiella, Pseudomonas, Listeria, Mycobacterium tuberculosis, Mycobacteria avium intracellulare, eg Lecinia, Francisella, Pasteurella, Brucella, Clostridia, Pertussis, Bacteroides, Staphylococcus, Streptococcus, B-hemolytic Streptococcus, Corynebacterium, Legionella, Mycoplasma, Eurea Plasma, Chlamydia , Gonococcus, Meningococcal, Haemophilus influenzae, Enterobacteriaceae, Proteus vulgaris, Proteus mirabilis, Helicobacter pylori, Treponema palladium, Borrelia burgdorferi, Recursive borelia, Rickettsia pathogens, Nocardia, and Actinomycetes It includes.

Representative fungal infectious agents that may be detected and / or determined by the present invention include, but are not limited to, Cryptococcus neoformans, Blastomyces dermatitis, Histoplasma encapratum, Coccidioides imides, Paracoccidioides brasiliensis, Candida albicans, aspergillus fumigautus, crude fungi (rispus), sporotrix hunky, chromomaicosis, and maturazine.

Representative viral infectious agents that can be detected and / or determined by the present invention include, but are not limited to, human immunodeficiency virus, human T-cell leukemia virus, hepatitis virus (eg, hepatitis B virus and hepatitis C). Virus), Epstein-Barr virus, cytomegalovirus, human papilloma virus, orthomyxo virus, paramyxovirus, adenovirus, corona virus, labdovirus, polio virus, toga virus, field virus, arena virus, rubella virus , And Leo viruses.

Representative parasitic agents that can be detected and / or determined by the present invention include, but are not limited to, tropical malarial protozoa, tropical malaria, trigeminal malaria protozoa, oval malaria parasites, and wormworms (Onchoverva volvulus) ), Lishumania, Trypanosoma spp., Schistosomiasis, dysAmoeba, Cryptosporidium, Giardia, Trichymonas spp., Balatidium coli, Vancroft worm, Toxoplasma spp.), nymphs, roundworms, whipworms, medinaworms, arachnoids, ganglion flies, Taenia spp., alveolar worms, and American worms.

The present invention may also be useful for detecting and / or determining drug-resistant bacteria by infectious agents. For example, vancomycin-resistant enterococci, methicillin-resistant Staphylococcus aureus, penicillin-resistant pneumococci, multidrug resistant tuberculosis bacteria, and AZT-resistant human immunodeficiency virus can be identified by the present invention.

In addition, genetic diseases may be detected and / or determined according to the method of the present invention. This can be done through prenatal or postnatal examination of chromosomal and genome abnormalities or genetic diseases. Examples of detectable hereditary diseases include, but are not limited to: 21 hydroxylase deficiency, cystic fibrosis, fragile X syndrome, Turner syndrome, Duchenne muscular dystrophy, Down's syndrome or other trisomy, heart disease, single hereditary diseases, HLA Type classification, Phenylketonneemia, sickle cell anemia, Tay-Sachs disease, thalassemia, Klinefelter syndrome, Huntington's disease, auto-area diseases, lipid accumulation, obesity defects, hemophilia, congenital metabolic disorders, and diabetes Include.

Cancers that can be detected and / or determined in accordance with the methods of the invention generally include oncogenes, tumor suppressor genes, or genes related to DNA amplification, replication, recombination, or repair. Examples of these include, but are not limited to: BRCA1 gene, p53 gene, APC gene, Her2 / Neu amplification, Bcr / Ab1, K-ras gene, and human papillomavirus types and 18. Various aspects of the invention can be used to identify amplification, multiple deletion and point mutations and microdeletion / insertion of the gene in common human cancers such as: leukemia, colon cancer, breast cancer, lung cancer, prostate cancer, Brain tumors, central nervous system tumors, bladder tumors, melanoma, liver cancers, osteosarcomas and other bone cancers, testicular and ovarian cancers, head and neck cancers, and cervical cancers.

In the field of environmental monitoring, the present invention relates to pathogenic and indigenous microorganisms in, for example, natural and modified ecosystems and microcosms, for example in municipal wastewater purification systems and contaminated areas where water purification or biological improvement is underway. It can be applied to detection, identification, and monitoring. It is possible to detect gene-containing plasmids capable of metabolizing biological foreign bodies, to monitor specific target microorganisms in population studies, or to detect, identify, or monitor genetically modified microorganisms in environmental and industrial processes.

The invention also relates to a number of forensic fields, such as identification, military and family relations analysis, HLA conformity classification, and blood, semen, or transplant organs for military personnel and criminal investigation. Applicable to screening for contamination investigations.

In the food and feed industry, the present invention is widely used. For example, it can be used to identify and characterize production organisms such as brewer's yeast, such as beer, wine, cheese, yoghurt. Another field of use relates to quality control and certification of products and processes (eg, livestock, pasteurization, and meat processing) for contaminants. It can be applied to the identification of the specific, plant-specific pathogen presence of plants, bulbs, and seeds, and to the detection and identification of veterinary infectious agents for other breeding purposes.

Examples

Example  1: particle synthesis

This example shows that various particles that can be used in accordance with the present invention can be synthesized. Exemplary methods are described in detail below.

Exemplary particle fractions were synthesized in polydimethylsiloxane (PDMS) microfluidic channels, 38-um in height, by stop-flow etching. For 12-multiple studies, the cord and inert buffer regions were 35% (v / v) poly (ethylene glycol) diacrylate (MW = 700 g / mol) (PEG-DA 700), 20% poly (ethylene glycol) (MW = 200 g / mol) (PEG 200), 40% 3 × Tris-EDTA (TE) buffer (pH 8.0), and 5% Darocur 1173 photoinitiator monomer solution. 1 × TE and rhodamine-acrylate (1 mg / ml) were added to the cord monomer so that the final concentrations were 9.4% and 0.6%, respectively. 1 × TE and blue food colorant were added to the buffer monomer so that the final concentrations were 8.0% and 2.0%, respectively. Food coloring agents were used to make the stream widths visible. 18% (v / v) PEG-DA 700, 36% PEG 200, and with addition of acrite-modified DNA probe sequences (Integrated DNA Technologies, IDT) suspended in 1x TE to achieve the desired final concentration of probe, and 4.5% Darocur; The remaining component polymerized the probe regions from a monomer solution that was 3 × TE.

To roughly match the target binding rate in this exemplary study, probe sequences were included in the particles at different concentrations ( Table 1 ). Since the target consumption characteristic time depends on the inverse square root of the probe concentration, it is necessary to quadruple the probe content included in the probe region of fixed size in order to double the binding rate for a given target. All binding rates in this exemplary study were corrected to match the case of let-7a binding. Without being bound by any particular theory, it is contemplated that higher sensitivity and short-term analysis can be achieved by maximally loading probe concentrations. In this particular case, the goal was to develop a 12-multiple assay with a wide dynamic range and ˜1 amol sensitivity for all targets.

TABLE 1 Exemplary particle codes and probe information of synthesized portions for 12-multiple studies. The final composition (v / v) of PEG-DA 700, PEG 200, and Darocur 1173 photoinitiator in the prepolymer stream for the probe was fixed at 18, 36, and 4.5%, respectively. Hairpin melting points calculated for DNA-RNA double strands by IDT's OligoCalc application for culture conditions in this exemplary study are listed in low order. For each miRNA, relative binding rates were calculated from the average target signals of solutions cultured 30- to 60-min with 500 amol target and linkage label. Short term cultures were chosen to ensure that the system did not reach equilibrium. Probe concentrations mentioned refer to prepolymer stream composition. About 11% of the probes in the prepolymer stream were covalently bound to the particles (Pregibon, DC et al ., Anal . Chem . 81, 4873-4881 (2009)).

Modified pipette tips (Biosciences) were used as delivery chambers and pressurized 4.5 psi was applied to load the cord, buffer, and probe prepolymer solution into the four-sphere microfluidic synthesis channels. Hydrogel microparticles (250 x 70) at speeds up to 16,000 per hour with 100-ms UV exposure (75% set Lumen 200, Prior Scientific) controlled by a shutter system (Uniblitz, Vincent Associates) interfaced with custom Python automated scripts x 35 um) were synthesized, coded, and functionalized simultaneously. The stream widths were adjusted so that the cord and probe regions were 140 and 40 um long, respectively. The remaining length of 70 um corresponded to the buffer regions. It has been shown that the same particle dimensions can easily accommodate two probe bands without affecting incubation, labeling, and scanning efficiency.

After polymerization, the particles were removed from the synthesis channel and recovered in 1.7-ml Eppendorf tubes containing 950 ul TET (1x TE with 0.05% (v / v) Tween-20 surfactant (Sigma Aldrich)). Tween was added to prevent particle agglomeration. 200 particles Suspension in PEG 200 for 5 minutes and then 700? Washed with TET. This washing sequence was also applied when washing particles of unreacted PEG-DA, probes, and rhodamine. The wash was repeated two more times and the supernatant centrifuged with dense particles was manually aspirated. The particles were stored in TET at final concentrations -12.5 particles / ul in a refrigerator (4?).

Example  2. miRNA  Culture experiments

This example shows typical sample culture steps suitable for use in the present invention.

In all exemplary cultures, prior to use, for example, the particles synthesized by the methods of Example 1 were transferred to room temperature and placed in a 0.65-ml Eppendorf tube with a final salt concentration of 350 mM NaCl and all particles of 12 types. Each was incubated in a total volume of 50 ul (˜360 particles / culture tube). For calibration and specificity studies, hybridization buffer (TETs of identification-specific NaCl moles) was added to the Eppendorf tube first, followed by all relevant target sequences (IDTs) diluted with 1 × TE and 500 mM NaCl mixture. Tweens were excluded from the dilution buffer to prevent inaccuracies in the pipette steps due to surfactant-induced wettability alterations. Depending on the type of identification, 1 ul TET or 1 ul E. coli total RNA (200 ng / ul) was introduced. For tissue profile studies, hybridization buffers were added directly to tubes containing 2.5 or 1.0 ul of pre-extracted and frozen total RNA (per tissue type; stored at 100 ng / ul, respectively). Primary sample pairs consisted of total RNA isolated from primary tumor and adjacent normal tissue. TRIzol purification separated the total RNA for all tissues; Intact 18S and 28S ribosomal RNAs were checked to confirm the integrity of isolation. Lung samples (BioChain) were taken from 50-year-old men with low differentiated squamous cell carcinoma. Breast samples (BioChain) were taken from 53-year-old women with severely differentiated invasive lobular carcinoma. Stomach samples (BioChain) were taken from 70-year-old women with low-differentiated adenocarcinoma. Pancreatic samples (BioServe) were taken from 65-year-old women with highly differentiated acinar cell carcinoma. In all exemplary assays, the total content of the synthetic sequence was set to 100 amol by measuring scanning / labeling consistency and introducing 1 ul miSpike (IDT) diluted appropriately in 1x TE with 500 mM NaCl for quantification purposes. Prior to the addition of the particles, the culture mixture was heated to 95 ° for 5 minutes in a Multi-therm shaker (Biomega) and left at room temperature for 7 minutes. The previously prepared master mix particles (18 per ul) were completely vortexed for 1 minute and 20 ul (-30 particles per each probe type) were introduced into each culture tube. The incubator (Quantifoil Rio) was incubated with the target for 90 minutes at 55 ° C. at a mixing speed of 1800 rpm.

After hybridization with the target, the samples were washed three times with 500 ul TET solution containing 50 mM NaCl. The particles were centrifuged and then the supernatant was manually aspirated from the tube. Nearly 50 ul of solution was aspirated after the third wash. Next, 245 ul of pre-assembled ligase master mix (100 ul 10 × NEBuffer 2, 875 ul TET, 25 ul XXXATPcarrier, 250 pmol ATP, 40 pmol universal adapter, and 800 U T4 DNA ligase) was added to the tube. The mixture was placed on a Multi-therm shaker at a mixing speed of 1500 rpm for 30 minutes at 21.5 °. After the ligase reaction, the same 3-wash cycle was performed. Streptavidin-r-phycoerythrin reporter (SA-PE, 1 mg / ml) was diluted 1:50 in TET and added to a final 1: 500 dilution. Samples were incubated at 21.5 ° C. for 45 minutes in a Multi-therm unit. After another 3-wash cycle, the particles were further washed in 500 ul PTET (5x TE with 25% (v / v) PEG 400 and 0.05% Tween-20) and suspended in a final volume of 50 ul PTET for scanning. . Prior to use, all PTETs were ground for 5 minutes to remove polymer aggregates.

Example  3. Detection using multi functional particles

In this example, hydrogel particles were used. Chemical and genetically complex hydrogel microparticles can be synthesized using flow etching techniques described in detail in US Pat. No. 7,709,544.

By polymerizing across the monomer stream co-laminar flow, multi-functional particles with chemically distinct regions can be produced quickly (> 10 ⁴ / hr) with high reproducibility. Separate "code" and "probe" regions are used to identify particles and capture targets, respectively. Bulk-immobilizing probe molecules on bio-inert, PEG-based gel supports provides solution-like capture kinetics and high specificity and sensitivity, applying surface-based immobilization strategies to microarrays and existing particle systems. More significant advantages. Unpolymerized holes patterns in the particle code section serve as a schematic multiplexed barcode basis to identify probe (s) in a particular particle. Unlike that use optical Unlike bead-based systems that use spherical optical coding, monochromatic scanning is possible due to the arrangement of the particles with multiple discrete regions, requiring only one excitation source and one detector ( FIG. 8A). ). In addition, the code library is easily extended to accommodate high levels of sample multiplexing or parallel processing. Other methods can also be implemented as described above for encoding these particles; For example, particles may have bands having variable fluorescence intensities (of one or more wavelengths), optical properties, dimensions, and the like.

In addition to the cords, the particles have a probe region in which targets to be quantified are captured. Probes typically consist of biomolecules that specifically bind to a target of interest. For nucleic acid detection, probes typically consist of DNA oligonucleotides. Appropriate DNA probe design and labeling methods are applied for post-hybrid labeling methods capable of operating gel particle scanning systems for high efficiency multiple miRNA quantification. In the discussion below, particle synthesis, culturing, and scanning steps are described in detail with respect to miRNA quantification, but this is provided only as an example, and these techniques are broadly applicable to nucleic acids and are contemplated herein.

Post-hybrid labeling schemes and suitable scanners, such as slit-scan systems, allow for rapid, multiplex analysis of nucleic acids using encoded particles ( FIGS. 8B and C ).

In some embodiments, the particles are designed such that the fluorescence signal quickly scanned in the fluid flow system and thus obtained is irradiated across the particle width by the detector. Each of the particles has a fluorescent code-region, a negative control region with a series of holes used for particle identification, and at least one probe region where the targets are captured and labeled. The size of the holes in the code area determines the depth of the marking fluorescent troughs and thus identifies the particles. By optimizing the particle structure and hole design ( FIG. 9 ) four distinguishable code levels (0-3) can be obtained in 70-um wide particles, thus 192 potential codes for 5-bar particles. It was found that they can be formed ( FIG. 8C ). Multiplexing performance can be easily increased to> 10 ⁵ by using multiple fluorescence levels for the code region or by adding more bars by including multiple probes in each particle. A decoding algorithm written in MATLAB was developed and applied to correctly decode the particles and quantify the targets. Any suitable decoding technique can be utilized. In this example algorithm, particle orientation (code- or probe-first) and velocity were determined to analyze the code holes and to primarily identify the code. The improved allocation is calculated by checking the consistency of the holes identified at the same level, and then the decryption confidence score is used to allow and reject the particles. The method typically provides ~ 98% decoding accuracy with only ~ 10% score-based rejection at throughput up to 20 particles / s.

Example  4. After- Hybridization  Cover

To generate a detectable signal indicative of the presence and capture of nucleic acid targets, an exemplary post-hybridization ligase-based method is provided and described in this Example and Example 5 for labeling.

This post-hybridization method can be used to fluorescently label selective targets bound, for example miRNA targets. Current methods rely on RNA bulk-labeling using chemical or enzymatic means. These methods suffer from high cost, the need for small-RNA purification and purification, sequence bias due to secondary structure, or complex, time-consuming protocols. Provided herein is a two-step method of efficiently labeling targets after hybridization, eg within about 1 hour.

Experimentally, T4 DNA ligase ( FIG. 10 ) was used to bind a universal oligonucleotide adapter to the 3 'end of targets captured in gel-embedded DNA probes that act as ligase templates. Thus, multiple targets can be labeled using a common, universal adapter in a single reaction. The labeling process requires only a few simple steps. First, the particles are hybridized with a sample, in this case total RNA, to capture suitable targets in the particle probe regions. After the excess sample is washed, a ligase mix containing suitable enzymes, all important cofactors (eg ATP), and a common biotin binding adapter are added. After a short reaction at room temperature (typically 5-60 minutes), any unreacted adapters are washed off using low-salt buffer. After removing the unreacted adapter, the particles are incubated with phycoerythrin-complexed streptavidin reporter (SA-PE) that provides fluorescence. After washing again, the particles are analyzed. More importantly, this labeling method is very efficient, there is no minimum RNA input requirement, and showed no sequence bias for the targets used in this exemplary study (Examples 4 and 5). For each new miRNA target species, the target-specific sequence was included in the universal probe template; No complicated deformations and individual fittings were necessary.

In this manner, adapter sequences were designed to minimize probe hairpin formation that could inhibit target hybridization and provide an adapter-probe melting point T _m of ˜10-20 ^° C. in ligase buffer. Although mild salt buffer was used in the washing process, dehybridization of the unreacted adapter applied any conditions that would destabilize nucleic acid interactions (low salt, high temperature, additives such as DMSO, PEG, or glycerol, etc.). Can be achieved. Typically, SA-PE reporters are used to obtain the maximum fluorescence signal. Additionally or alternatively, ligase-based labeling can be performed with adapters labeled directly with phosphors or other reporting entities. Without being bound by any particular theory, this reduces analysis time and complexity. This treatment can be used to design suitable probes and adapters to connect the adapters to the 3 'end of a DNA or RNA species having 5' phosphorylation at the 3 'OH or 5' end.

Example  5. Linkage Enzyme-based Labeling Optimization and Modifications

In various embodiments, several aspects of the labeling method described herein were optimized, including probe / adapter design, reagent concentrations, wash buffer salt component, ligase reaction temperature, and ligase reaction temperature. Here, the ligase reaction time and the length of the adapter tail show the effect on labeling efficiency. Nucleic acid probes, targets, and adapters (all Integrated DNA Technologies, IDT) are shown in the table below.

Table 2 : Nucleic Acid Probes and Targets Used in Optimization Studies. The bold sequence is the universal adapter-specific sequences, the normal sequence is the target-specific sequences, and the underlined sequence is Poly (A) tails.

Adapter / Probe Design

The exemplary probes, including miRNA-specific regions and adapter-specific regions, were designed such that when bound, the 3 'end of the miRNA target was adjacent to the 5' end of the adapter. When using a DNA template, it is known that the T4 DNA ligase that binds DNA to RNA molecules proceeds several times faster at the 3 'end of the RNA than the 5' end (Bullard, DR et al . , Biochem J 398 , 135-144). (2006), 3 'end labeling of miRNA targets was selected. Adapter sequences and lengths range from (1) melting point in ligase buffer to 10-20C, and (2) sequences are not significantly self-complementary to avoid adapter hairpin or homodimer formation, and (3) (adapter and miRNA Complete DNA probes (with sequences) were chosen to not form significant hairpins for the test miRNA.

Ligase reaction time

let-7a was used as a model system to determine the minimum ligation time required for this labeling assay. Particles with let-7a DNA probe region were incubated with 5 fmol synthetic let-7a RNA at 55C for 110 min. The particles were washed three times with phosphate buffered saline containing 0.05% Tween-20 (PBST, pH 7.4, Fluka) and 200 U T4 DNA ligase, 40 nM Cy3-modified adapter in T4 DNA ligase buffer (NEB). UA10-Cy3), and 250 l of a ligase reaction mix containing 0.05% Tween-20 and incubated at 16C for 10, 30, or 90 minutes. After the ligase reaction, the particles were washed three times in TE containing 0.025 M NaCl, placed on a glass slide and imaged with a CMOS camera (Imaging Source). Fluorescence intensity was measured in the probe region of each particle, and background fluorescence was subtracted to obtain a target signal indicating the efficiency of the linkage enzyme reaction. The results are shown in FIG.

Relative efficiency was calculated by normalizing each signal with the signals obtained for a 90 minute sample. As shown in FIG. 11, the ligase reaction was> 95% complete even after a short 10-minute reaction. For the experiments described in this study, a ligation time of 30 l was applied to ensure a nearly complete ligation reaction.

For biotin binding adapters Tail length

Reported streptavidin-phycoerythrin (SA-PE) is a large protein construct with a turn radius of ˜10-15 nm. Thus, when using biotin binding adapters with SA-PE reporters, it has been found to be advantageous to extend the biotin group from the gel matrix polymer backbone. To this end, a poly (A) tail was used at the adapter 3 'end and the effect of tail length on the target signal was investigated.

In this experiment, the same let-7a particles were used as in the above section. Incubated at 50C for 60 minutes with 50amol let-7a miRNA. The particles were washed three times in PBST and dispensed into four separate tubes. Particles in each tube were washed with 200 U T4 DNA ligase in 1 × T4 DNA ligase buffer (NEB) containing 0.05% Tween-20 at room temperature for 30 minutes, and 40 nM UA10-bio (0, 3, 6). Or a 12 bp poly (A) tail). After ligase reaction, the particles were washed three times in TE containing 0.05 M NaCl and 0.05% Tween-20, placed on a glass slide and imaged with an EB-CCD camera. By comparing the target signals as shown in Figure 12 Poly (A) tail length influence was determined.

As shown in FIG. 12, the poly (A) tail length has a great influence on the acquired target signal. From 0 to 12 bp, the signal increases by ~ 5x, but seems to be unchanged at this point. For the experiments described in some examples, universal adapters with a poly (A) tail length of 12 bp were used.

In various embodiments, a wide variety of alternative technologies and systems can be successfully applied. Such embodiments are provided.

Direct adapter-based labeling with phosphor-binding adapters

Instead of using a technique where biotinylated adapters are linked by a ligase reaction and then reported as streptavidin-binding phosphors, the phosphors can be used directly. When linked to the 3 'end of the hybridization targets, universal adapters may preferably contain the desired phosphor at the 3' end or at one of the internal nucleotides. As described in Example 13 , the method reduces processing steps by one, which allows for simpler and faster processing.

Multiplexed detection using adapters with different phosphors

In some applications, it is important to detect multiple nucleic acid species in a common region. When the probes are not separated in the distinct regions of the particle or substrate, multiple detection can be performed using adapter variants with phosphors in the native emission spectrum. For example, three probes each with a unique adapter probe sequence can be used with adapter variants with three unique phosphors in one region. This embodiment is shown in FIG. 14 .

Alternatively, in some applications it is important to detect the variability of the target terminus (eg, targets with truncated nucleotides at one terminus). In this case, a similar probe is used, but a large number of adapters (preferably with different phosphors) are used which extend different numbers of nucleotides to the target probe region. Only the ligase reaction proceeds when the target / adapter ends are completely contiguous, so the target end sequence (s) are determined by measuring the respective phosphor levels used for the various adapters. Alternatively, adapters with the same phosphor may be used in two separate quantification steps (in two samples) in parallel or sequentially (in the same sample but in two ligase reaction steps).

Both labeling and universal coding, particularly when all involved species are DNA, ligase reactions can be achieved at the 5 'or 3' end of the adapters. When using DNA ligase, ligase reactions are known to be more effective at the 3 'end of the RNA target (ie, the 5' end of the DNA adapter). Adapters can be DNA, RNA, or any type of nucleic acid analog. Nucleotides of adapters or probes may be modified, such as submerged nucleic acids.

Use of other functional adapters

While the phosphors were used for coding and labeling in the experiments, it should be understood that other types of functional species may be used, including but not limited to: chromophores, radioactive species, magnetic materials, quantum dots, and the like. It should also be understood that general purpose coding can be achieved using adapters with intermediary species (eg biotin), and that functionalization (eg fluorescence) can be added in additional steps. Adapters can have a phosphor at the end of the construct or by varying the backbone (eg fluorescent nucleotides). Another way is to use insert DNA / RNA dyes (eg PicoGreen, YOYO-1, etc.) to introduce fluorescence in general purpose coding or labeling. They are used with enzymes such as nucleic acid terminal hydrolases that selectively degrade nucleic acid species that are not cleavage protected. In this case, adapters with longer sequences or more secondary structures give brighter signals from the dyes. In other cases, the adapters may also have specific nucleic acid sequences (tags) targeted in a continuous process to add fluorescence (eg, using phosphor-binding complementary oligonucleotides).

No-cleaning ( Rinse - free Cover

It is possible to apply ligase-based labeling techniques for particle analysis in a wash-free manner. In one embodiment, the ligase reaction proceeds at a lower temperature (eg, adapter melting point, below Tm) than scanning / analysis (implementing above adapter Tm). Adapter melting points are adjusted through sequence, salt concentration, submerged nucleic acids, and the like to denature from probe templates to temperatures below, near or above the temperature used for particle analysis. The ligase reaction and scanning can be implemented at adapter Tm or slightly above the temperature—this also allows ligase reactions with a minimal residual adapter associated with the probes during the assay (possibly reduced efficiency).

Example  6. Particle Scanning

Typical scanning methods suitable for using the present invention are described in this embodiment.

The focusing mechanism (35 um in height) with two inlets, one outlet, four side streams, and a 125-um wide detection zone is equipped with a Zeiss Axio Observer equipped with a Zeiss Plan Neofluar 20x objective (NA 0.50) Mounted on microscope (FIG. 9A) (Chapin, SC, et al ., Lab Chip 9, 3100-3109 (2009). Insert a chromium-coated soda lime glass mask into the iris slider bar and into the microscope aperture to insert a 100-mW, 532-nm Laser Lasers beam spot 4 x 90 Limited to um thin excitation window. Prior to each scanning, laser alignment was calibrated with a power meter (Newport, Model 1815-C). Using an image acquired with a Clara Interline CCD camera (Andor Technology), the excitation window was aligned so that the long dimension was perpendicular to the flow direction at about 750 um from the instrument outlet port. A photomultiplier tube (PMT, Hamamatsu H7422-40) was used to record the fluorescent indications of the CCD and passing particles using a conversion box at the side port of the microscope.

PTET serving as focal sheath stream was injected from the reservoir inlet. In each trial, the particle-containing fluid was aspirated into the modified pipette tip using a syringe connected to the tip through a Tygon tube. The tip was inserted into a suitable PDMS inlet port and both fluids were flowed at pressurized 8 psi. Scans for 50 ul of particle-containing fluid were typically maintained at ˜30 s and used less than 25 ul of sheath fluid. Depending on the number of particles used in the analysis, particle throughput was in the range of 5-25 per second. The instruments could be used more than 50 times without deterioration. After each scan, 30 ul 1 × TE of washing solution was passed through the particle inlet to eject trapped particles and to reduce contamination between runs. In addition, the loading tip can be washed and reused with ethanol and water. Manually loaded from Eppendorf tubes, eight samples were scanned and analyzed in 30 minutes, and the expected throughput of ˜125 samples was reached in 8-h operation. In future applications of the present technology, the efficiency will be further increased (> 500 samples / day) with particle-loading automation and washing procedures using well-plates and computerized liquid treatment systems.

A self-contained amplifier with low-pass filter regulated the PMT output current and captured the generated voltage signal at 600 kHz with a digital acquisition (DAQ) board (USB-6251, National Instruments). A script written in Python was used to convert each scan into a binary text file for off-line analysis. Optimized scanning system performance by scanning single-chemical particles containing fluorescent rhodamine everywhere, with amplifier gain 22, cutoff frequency (100 kHz), slit with highest signal-to-noise ratio (SNR) and frequency response A combination of width (4 um) and PMT control voltage (0.300 V) was obtained. In addition, by scanning particles of various barcode designs, it was found that a minimum spacing of 8 um between holes was required to prevent mechanical deformation of the soft hydrogels in the flow alignment process. A four-level code design was applied based on studies that systematically changed the hole size to determine the effect on bone depth in scan profiles ( FIGS. 9B and C ).

Example  7: Data analysis

Typical data analysis by the present invention is described in this example.

Raw data files (20 million dots / scan) generated by the scanning process are analyzed with a custom written MATLAB algorithm designed for separating individual particle marks, identifying the code represented by each particle, and quantifying binding target content. The algorithm processed a scan of 50-ul samples in 5 s, and the method is suitable for high efficiency applications. In the first filter step, the algorithm extracts scan portions that exceed the threshold voltage and examines whether each feature is identified by the particle representation for the extraction zone. Using fluorescence code region specific properties as reference points, an estimate for each particle velocity with high-reliability is determined and utilized to pinpoint the valley positions for the five code holes. Particle orientation ( ie , probe- or cord-first) was set using fixed-value “3” holes bounded by inert buffer regions. After the initial code identification is calculated from the bone depth, the bone depth standard deviation of the designated holes at the same level is measured and secondary reviewed and corrected if necessary. In the final decoding step, the confidence score for the particle is calculated by calculating the correlation linearity between bone depth and allocation level. If the Pearson coefficient is 0.97 or less, particle decoding is rejected.

In order to calculate the binding target content, the measured particle velocity is used to infer the probe region center position. For simplicity, a search box is used to examine the scan in this area and search to identify local maximums that can be correlated with the target-binding phenomenon. If a maximum is found, the search window position along the scan profile is adjusted until the two endpoints are sufficiently closed at the signal amplitude, so that the nearly symmetric maximum portion that is averaged for quantification purposes is selected. If no maximum is found, the mean signal is calculated using the original estimate for the probe center without a search box. To calculate the background for a given probe sequence and culture conditions, for example, the same synthetic portions of particles are cultured in the presence of only 100 amol of miSpike target by the above procedure. The method provides probe-dependent background measurements derived from the PEG support and universal adapters used in the labeling process. In addition, in all code identification and target level calculations, particles are considered if the target level is greater than the 3/4 quartile upper or quartile lower 1 quartile range of the data set consisting of target levels associated with the probe. It doesn't work. This measurement is taken as an additional protection against correct code assignment and inter-run contamination.

For calibration and profile studies, background-deleted mean signals were calculated for each target at each culture condition. For a run-to-run comparison of the calibration data, the signals are normalized by miSpike amplitude background-rejected with empty (0 amol) samples that provide 100-amol miSpike reference values for the examination of both neat and E. coli. It was. The miSpike target values shown in the calibration curves ( FIGS. 15 and 16 ) were not adjusted to this criterion to show labeling and scanning process reproducibility. For the profile study, the background-cleared miSpike signal by the first scan for each healthy tissue was used as a reference for this tissue analysis. Given profile scan signals were further normalized to RNU6B content in this scan to allow direct quantitative comparison independent of total RNA content. Tissue analyzes were run repeatedly at least one day after the initial date. For each calculated expression rate, healthy tissue and weigh samples were analyzed and scanned in the same set of experiments for consistency. In order to calculate the expression ratio, a target of at least 2 amol was required to be detectable in a given pathological tissue. Since only a single patient sample was used for each tissue type, a threshold mode was implemented to determine dysregulation. For each target in each tissue, SNR was calculated by dividing the set mean by the standard deviation using three log-transformation expression ratios from three separate trials. Targets with three or more SNRs were considered overregulated. In all 20 cases dysregulation could be correlated with observations in the literature related to expression profiles of mature miRNA (16 of 20) or miRNA precursors (4 of 20).

Example  8: miRNA  profile

The experiments described in this example show that the compositions and methods provided herein can be used in a variety of applications (eg, miRNA profiles).

Experimentally, this technique was demonstrated by examining dynamic range, sensitivity, and specificity in a 12-multiple assay that specifies 10 clinically relevant miRNA targets. RNU6B was used as an internal control for normalization purposes due to relative invariance depending on tissue type and disease state. In addition, 100 amol miSpike (synthetic 21-mer) was used as an external control to verify the consistency of labeling and scanning treatments. Twelve portions of single-probe particles were synthesized for this study. To compensate for target hybridization differences, coarse rate-matching was made by adjusting the probe concentrations for each target (Table 1) using a predetermined scaling law. To fully show scanner versatility, a 60-multiple analysis was simulated by associating five individual codes with each probe type particle.

To further assess the sensitivity and dynamic range of the system, four of the 12 targets were added simultaneously to the 50-ul culture mixtures at a content of 1 to 2187 amol. A linear detector response was observed for 4 logs and 200 ng E to achieve sub-atomol sensitivity for 3 of 4 targets and add neat samples and complexity. . coli between the total RNA sample is added a significant match (Fig. 15 and 16). In comparison, existing bead-based methods have a 200-amol detection limit and only one log range. To assess specificity, four members of the let-7 line added at 200 amol each to samples containing let-7a particles and 200 ng E. coli total RNA were analyzed. Scanning results show a maximum cross-reactivity of 27% ( FIG. 15B ), which is lower than other systems (microarray ˜50%) and can be significantly improved with lower hybrid salt concentrations ( FIG. 17 ). This analysis showed very high reproducibility with intra-run and inter-run COVs of 2-7% ( Table 3 ). Due to detection and particle manufacturing limitations, bead-based systems users generally apply 4,500 copies of each type of beads in the analysis for high-reliability estimation of target levels. In contrast, it was found that only 10-15 hydrogel particles were sufficient for each probe type ( FIG. 18 ).

Table 3: E. coli Target-on-run COV at the calibration curve. All values are percentages calculated statistically using an average of 19 particles. miR-222 showed a detection limit above 1 amol. The run-to-run COV for the background-removed miSpike signal (100 amol) for the nine display scan settings was 6.84%.

Further validation of the platform performed several types of tumor expression profiles across tumors and adjacent normal tissues. As expected, dysregulation of several miRNA targets was observed for all diseases examined ( FIG. 15C, Table 4, and Table 5 ). Although 250 ng total RNA was used for these samples, similar results were obtained for lung samples using only 100 ng, suggesting that low input RNA is sufficient. With a total analysis time of just 3 h, the profile is more efficient than the microarray (~ 24 h) approach and much better sensitivity and reproducibility than current bead-based methods.

TABLE 4 Average target contents and run-to-run target content COV for 250-ng tissue profile iteration validation. The upper value of each item is the average content (amol) for repeated attempts; Figures in parentheses below are COV (%) between runs. The contents were determined in comparison to the 100-amol miSpike signal that was background-depleted from each run. Repeated analyzes were performed on different days to strictly test reproducibility. Each statistic was calculated using an average of 16 particles. No data indicates no target exists above 2 amol cleavage.

Table 5 : Log-transformation expression ratio for 250-ng assay. The upper value of each item is the average of the log-conversion ratio of tumor content-to-health tissue content of the indicated targets over three trials in a particular tissue; The numbers below in parentheses are the standard deviations. Red items indicate more than adjustment. Items without data indicate that the ratio was not calculated.

This highly efficient nucleic acid profile system and platform thus demonstrates the application of a versatile scanning and labeling method that enables the use of schematic-encoded hydrogel microparticles. The system's unprecedented sensitivity, flexibility, and throughput combinations offer surprising possibilities for screening and clinical applications, especially for quantification of low-water miRNAs and other biomolecules in readily available media such as serum.

Example  9: Scanning multi-developed particles

Examples showing that the method differs from standard cell assays are shown in FIG. 19 below. In this embodiment, the functional regions of the multi-functional particles carry the light scattering-inducing entities that cause the cytometer to trigger the development record.

The particle structure is shown with two coding regions and a single probe region where the target is captured. The two encoded regions have various levels of phosphors built in to give distinct fluorescent indications in the three fluorescent channels. One coding regions are intentionally wider than the other to indicate particle orientation. The target may be labeled with a phosphor, preferably shown in a single fluorescent channel, as shown. In this example, each particle will be reported in three phenomena. Of these three phenomena, the first and last ones give code information and the second one is used for target quantification. In this way, the code and the captured target are quantitated non-simultaneously.

Preliminary experiments showing the implementation of the method were conducted. Multifunctional particles of ˜200 × 35 × 30 mm dimensions were synthesized with two fluorescent regions (30 mm and 60 mm stained with Cy5 and Cy3 fluorescent dyes, respectively) placed on the side of the wide inactive region. The particles were run on an Accuri C6 cytometer with a flow rate of 100 ml / min and a core size of 40 mm. The threshold in FL4-H (Cy5 detection) was set to 100,000.

Each phenomenon recorded in the cytometer is given a time stamp of 1 ms resolution. Since the particles typically move the flow cell at a rate of ˜1 m / s, irradiation of 200 um particles is expected to last ˜0.2 ms. Thus, two phenomena recorded from a single multifunctional particle are expected to appear in the same time stamp. To show whether each particle is read as two separate phenomena, a histogram showing a time stamp count with a given number of phenomena is shown. The number of phenomena per time stamp is expected to be even for the present particles (2 phenomena for a single particle, 4 phenomena for two particles, etc.) and to be sipping for normal particles. As a control, a typical spherical form of standard Accuri 8-peak calibration beads was run. The results are shown in FIG.

Through the data acquisition process it can be seen that the calibration beads are scanned quite randomly, providing a range of 1-4 beads / time stamp. Multifunctional particles, on the other hand, show a group of 2 or 4 phenomena / time stamp, which fits very well with the theory that each particle is read into two phenomena. It can also be seen from the development versus time plot that there is a high- and low-level fluorescence reading in each time stamp process. The particles in the FL-2 channel are designed to have one bright and one dark region of fluorescence, which also supports the theory that each particle is read out with two discrete phenomena. This method can also be applied to three or more phenomena per particle. Each region / phenomena varies in fluorescence level, forward or side scatter, and width.

In some cases, it is useful to combine the differentiated levels of multiple phosphors into each encoded region of multiple functional particles. For technical verification, rod-shaped particles, 200 × 35 × 30 mm, with a single 60 mm coding area at one end were used. The encoded region was labeled using four distinct levels of Cy3 and Cy5 fluorescent dyes. Particles were analyzed with an Accuri C6 cytometer at a flow rate of 100 ml / min, core size of 40 mm, and a threshold of 5000 at FL4. The results are shown in FIG. 7 below.

The diagram of FIG. 7 shows that distinct fluorescent fingerprints can be generated in the coding region of each of the multifunctional particles. Each group of data points represents a separate code.

To analyze the data using this method, the phenomena are classified into particles, orient the particles, normalize the fluorescence, if desired, to a standard, and fluorescence, scattering, or developing in each code and probe region. An algorithm is needed to quantify the width. A confidence level is then given for the corresponding code for each particle, and those that are not called with a predetermined confidence level are excluded from the analysis. The fluorescence of the probe area is then used to determine the target content present in the test sample. The system can be easily automated using analysis performing software after or after the scanning process.

Example  10. Raw Signal Reading

This example shows the investigation of multiple functional particles in standard flow cytometers. In some embodiments, the irradiation is to acquire a signal from a cytometer detector, which is then processed into phenomena with the instrument's firmware and custom software to effect particle scan identification, orientation, and analysis. Three separate cytometers from Partec, Accuri (C6), and Millipore (Guava) were used to validate the technique for scanning particles.

Standard data acquisition (DAQ) boards, using leads (Partec and Millipore) or QC pins (Accuri) from each cytometer single PMT, connected via a simple circuit (sometimes only a single resistor), to collect raw data The voltage was measured using a National Instruments NIDAQ-USB6250. Custom scripts written in Python are used to communicate with the DAQ board, allowing the user to enter the number and frequency of samples. Samples were taken in the range of 60 kHz to 1 MHz. After acquisition, the data was stored in a single file.

For analysis, fast Fourier transform-based filtering was applied to isolate the desired frequency response for each scan. The threshold was then set to identify particles in each sample. If a signal is detected above the threshold for a predetermined number of samples, the region of interest and adjacent data points are stored as a single particle scan. Design features built inside each particle were used to identify the cord and probe regions. In addition, each signal was normalized by the features given to each particle. In the examples the barcodes consisted of a series of bands with different fluorescence levels along the particle.

A basic set of test particles was used to assess the alignment and consistency of the particle-to-particle scans in three commercial cytometers. Rod-shaped fluorescent particles with three distinct regions were synthesized. Static image scans of a normal fluorescence microscope were compared with those obtained from raw scans obtained in each instrument single PMT. After applying the FFT-based filtering to separate the desired frequency response for each device, the signal from each identified particle is scaled (x-axis only) and the common x-axis to compensate for velocity deviations. As shown. Typical results with overlapping particle scandals and development width distribution (correlation with particle velocity) are shown in FIGS. 21 and 22 .

Compared to static scans, it can be seen that all three cytometers can scan multiple functional particles at various levels of accuracy. In particular, Guava equipment showed very good reproducibility, but had rounded features due to the large laser spot size (˜25 mm) when compared to the respective feature dimensions. Accuri showed quite reproducible scanning, but with a lot of noise. Partec showed significant variation in scan intensity due to the laser spot size not reaching the entire flow cell, and mostly due to the particle brightness depending on whether the particles were placed in the cross section of the flow cell.

Nucleic Acid Detection Nucleic acid detection was performed using particles having a single wide fluorescent region exhibiting a “barcode” and a small probe region flanked by two inactive regions. MicroRNA let-7a added at 1 fmol level in 50 ml reaction solution was detected by hybridization at 55C for 90 minutes. The bound target was labeled with streptavidin-phycoerythrin and the particles were scanned using Millipore Guava. Fluorescence levels in the particle probe area indicate the target content present in the assay. The results are shown in FIG.

Again, the results could be reproduced but showed signal rounding at the interface between the various particle regions. Analysis of the highest sensitivity will be obtained from green (532 nm) laser excitation.

Example  11.Maturity microRNA  Distinguishing Targets and Precursors

According to the invention, the probes can be designed to be labeled. This example shows microRNA detection using selective end-labeling to detect mature microRNA species without precursor species being detected.

Mature microRNAs were used which contain the entire sequence at one end of the precursor (3 'or 5' depending on the exact microRNA species). If labeling is performed at the end common to both the mature and precursor, both species are labeled and quantified. To selectively detect mature species, labeling takes place at the opposite end of the mature species of the sequence contained within the precursor. In this way, mature species can be detected without precursor detection.

To show detection of mature microRNA species only, synthetic miR-143 mature and precursors thereof were used. The miR-143 mature sequence appears at the precursor 3 'end. Sequences for these species are given in Table 6 below.

Table 6 : Mature and precursor miR-143 species sequences. The mature sequence is underlined in the precursor sequence.

Two doses of particles were used for this study-one with the miR-143 probe that labels the 3 'end of the target and the other with the miR-143 probe that labels the 5' end of the target. The probe and adapter sequences used in this study are shown in the tables below.

TABLE 7 Probe design labeling the 3 'or 5' end of mature miR-143 species. The sequence for mature miR-143 is underlined in each probe sequence and the remaining sequence is for capturing the designated adapter for labeling.

TABLE 8 Adapter sequences for 3 'and 5' labeling. Adapter 1 has a 5 'phosphate group and 3' biotinylation, and adapter 2 has a 5 'biotinylation.

Probes 1 and 2 were designed to label binding targets at the 3 'or 5' end of mature miR-143, respectively. For 3 'labeling, a DNA adapter was used and for 5' labeling, an RNA adapter was used. These provided the most efficient ligase reactions to designated ends of the RNA target.

At 55C for 90 minutes, the particles were incubated in a buffer containing 0.5M NaCl in TE with a 500amol mature miR-143, 500amol miR-143 precursor, or miR-143 free target. After hybridization, the particles were washed in TE containing 0.05M NaCl. The particles with probe # 1 were subjected to ligase reaction with T4 DNA ligase and 40 nM adapter 1 at 0.8 U / ul concentration. The particles with probe # 2 were subjected to ligase reaction with T4 DNA ligase 2 and 40 nM adapter 2 at 0.02U / ul concentration.

After 30 min ligase reaction at room temperature, the particles were washed with were rinsed with TE containing 0.05M NaCl and incubated for 30 minutes at room temperature with streptavidin-phycoetrine reporter diluted to 2ug / ml. After reporter binding, the particles were imaged with a fluorescence microscope. The signal-to-noise ratio, calculated as the mean signal divided by the signal standard deviation of the negative control sample, was calculated for each miRNA species and labeled form. The results are shown in the table below:

TABLE 9 Labeling experiment results using 3 'and 5' labeled forms for mature and precursor miR-143 species. Signal-to-noise ratio (SNR) represents the mean fluorescence intensity signal divided by the negative control signal standard deviation.

As can be seen, when probe # 1 is used with DNA ligase (Dnal) and adapter # 1, both mature and precursor miR-143 show detectable signals, although the precursors are much lower. When using RNA ligase 2 (Rnal2) and adapter # 2, only mature miR-143 is the only target that is effectively labeled, and precursor species are not detected above SNR = 3 (ND). This shows an effective detection difference for detection of mature miRNA compared to precursor species when the 5 'end of the target is labeled.

Example  12: Two-band coding with probe functionalization

This example showed that the compositions described herein can be synthesized and functionalized for coding, in particular for general purpose coding.

Stem-Loop Encoded Probe (SEQ ID NO: 26) (included with / 5Acryd / AATAAACACGGGAATAACCC, IDT, 10 uM) using stop-flow etching as described in US Pat. No. 7,709,554, incorporated herein by reference, negative control region , Rectangular particles having a probe anchor (SEQ ID NO: 27) (including 5Acryd / GATATATTTT, IDT, 50 uM), and a second negative control region were synthesized. The particles dimensions are ˜120 × 60 × 35 um and the thickness of each of the 4 bands is ˜30 um. Different ratios of fluorescently-labeled adapters (SEQ ID NO: 28) (5'-Phos-GTGTTTATAA-Cy3, IDT) to unlabeled adapters (SEQ ID NO: 29) (5'-Phos-GTGTTTATAA-invdT, IDT) The particles were incubated with. Each ligase mix contained 250 nM ATP, 200 U T4 DNA ligase (all obtained from New England Biosciences), and NEBuffer # 2 with a total of 40 nM encoded adapters. The ligase was carried out for 30 minutes at room temperature while mixing at 1500 rpm in a thermostat. The particles were then washed 3 × with TE buffer containing 50 mM NaCl and 0.05% Tween-20. Particles were imaged with a Nikon Ti-S microscope with a 20 × objective, NA = 0.5, and a CCD camera (Imaging Source). Fluorescence intensity scans were plotted according to particle length and fluorescence signals were measured and averaged for the five particles in each sample. Typical results are shown in FIG. 24.

The data show that labeling worked, but the fluorescence to adapter ratio relationship is not linear. This means that the hybridization or ligase reaction rates differ between the fluorescent and non-fluorescent adapters used. However, at the 100% level the images are saturated and it is difficult to use all four data points for comparison. Raw and adjusted data are shown in Table 10:

In addition, universal particles having two coded regions (with hairpin anchors) and a probe region (with a linear anchor), synthesized by the stop-flow etching method, were used. Particles are ~ 180um in length, 35um in width, and ~ 25um in thickness, 4 zones-U code 1 (composite at ~ 10 uM), U code 2 (composite at ~ 10 uM), inert, and U anchor (~ 50 uM) Synthesized in). The DNA sequences used in this study are as follows (Integrated DNA Technologies, 5-'3 '):

U-code1 probe = / 5Acryd / AAT AAA CAC GGG AAT AAC CC (SEQ ID NO: 30)

U-code2 probe = / 5Acryd / AAT AAT GTG CCC AAT AAG GG (SEQ ID NO: 31)

Ucode 1 Adapter Cy3 = / 5Phos / GTG TTT ATT A / 3Cy3Sp / (SEQ ID NO: 32)

U-Code 1 Adapter invdT = / 5Phos / GTG TTT ATT A / 3InvdT / (SEQ ID NO: 33)

U-Code 2 Adapter Cy3 = / 5Phos / CAC ATT ATT A / 3Cy3Sp / (SEQ ID NO: 34)

U-code 2 adapter invdT = / 5Phos / CAC ATT ATT A / 3InvdT / (SEQ ID NO: 35)

After synthesizing and washing the particles, ligation with 250 nM ATP (NEB), 200 U T4 DNA ligase (NEB), 0.05% Tween-20 (Sigma), and DNA adapter (below) in a total of 500 ul NEBUFFER # 2 (NEB) The enzyme reaction master mix was prepared:

F1: 80nM U-Code Adapter 1 Cy3

N1: 80 nM U-code adapter 1 invdT

F2: 80nM U-Code Adapter 2 Cy3

N2: 80 nM U-code adapter 2 invdT

In a 96-well, 1.2 μm filtration-bottom plate (Millipore), a mix of ligase reaction mixtures listed in Table 11 was added:

10ul particles were added to each month (˜200 particles) and the plate was placed in a mixer and mixed at 1500 rpm for 30 minutes at room temperature. The excess buffer was then extracted using a filter unit and washed 2 × with 200ul TE buffer of 0.05% Tween-20 (TET). For imaging, 60ul TET was added to each well, mixed for 30 seconds and pipetted 35ul from each well into a glass slide. Each sample was placed in the middle and covered with an 18 × 18 mm coverslip. Particles were imaged with a Nikon Ti-U microscope with an Imaging Source CCD camera with brightness = 30, gain = 600, exposure = 0.412 sec, gamma = 150. After imaging 5 particles per sample, ImageJ was used to orient and crop the image and attach the data to Excel for analysis. The raw data analyzed are shown in Table 12 below, and the ratios indicate the fluorescent adapter content used (where 1 = 100%):

25A and B show schematic particle design, sample fluorescence images due to each ligation reaction, and average scan of particles.

The measured fluorescence versus adapter content plots from each ligation reaction mix are shown in FIG. 26, where "Code 1" and "Code 2" represent the average signal of the first and second encoded regions, respectively. The encoding worked well. More importantly, the coding is specific; The signals for each coded region are independent of each other. As observed in the above experiments, the fluorescence level for each encoded region was not linear with respect to the fluorescence adapter content. The signals were very reproducible, especially at 25% fluorescent adapter levels.

Example  13: Universal coding with template functionalization

In this example, universal particles with different polynucleotide templates for encoding were prepared.

In the examples, particles were designed that have three active regions spaced by two inactive regions and that can be scanned with a commercial cytometer. DNA templates with acrylate modifications (denoted 5'acry) used for encoding are listed in Table 13 below:

These molds were used in the particle design shown in FIG. 27. Hydrogel particles made of poly (ethylene glycol) according to the present design were produced by the flow etching method. Particles were made from monomers having concentrations of the polynucleotide templates listed in Table 14.

For use in flow cytometry, UC2 templates are functionalized with Cy5 modified adapters to trigger phenomena in RED2 channels. For barcoded, UC1 and UC3 templates were modified with adapters (Cy3 modified, FAM-6 modified to achieve distinct fluorescence levels for barcodes in the cytometer YEL channel and distinct fluorescence levels for orientation in the GRN channel. , Or non-fluorescent). Adapter sequences used are given in Table 15 below:

The number of distinguishable fluorescence levels in each barcoded region depends on the encoding accuracy and the performance characteristics of the cell analyzer used. In order to determine the appropriate code dilution to maximize multiplexing in a given flow cytometer, several blends of fluorescent and non-fluorescent adapters can be attempted for a given coding template. Several ratios of fluorescence to non-fluorescence adapters were studied by logarithically changing the ratio between fluorescence and non-fluorescence and ligase reaction of multiple particle fractions to obtain the curve shown in FIG. 28. Template functionalization with adapters via ligase reaction was performed for all templates for 1 hour at room temperature using 0.8 U T4 DNA ligase per total ul for each encoding template (fluorescent or non-fluorescent), total 40 nM adapters. It was done concurrently.

Various dilutions of UC1-A-Cy3 in UC1-A-NF were used to functionalize universal particles to create titration curves for acquired fluorescence. The curve in FIG. 28 shows the log (fluorescence) obtained by applying the Cy3: NF adapter ratio in the range of 0: 1 to 1: 1. This curve was obtained by YEL fluorescence measurement of Guava easyCyte 6HT.

Using this method, titration curves were made for UC1 and UC3 templates with Cy3 modified and non-fluorescent adapters. Typical results showing log (fluorescence) are presented in Table 16 below.

Given the expected coefficient of variation (COV) of the signals measured here, the dilution used in the coding is selected such that the expected fluorescence levels are almost impossible to overlap with the adjacent dilution. To obtain 5 levels for each barcoded region, the following non-fluorescence to Cy3-modified adapters dilution of Table 17 was applied:

With the possibility of generating five levels of fluorescence separated in each barcode 1 and barcode 2, a total of 25 unique combinations are obtained. These dilutions were attempted with universal particles synthesized in this example. In order to differentiate the two encoded regions, higher levels of green (FAM-6) were added to a series of dilutions for barcode 2. Fluorescent adapters for UC2 are also included in the functionalization to generate a signal in RED2 that is used to trigger phenomena in the cytometer. Particles are functionalized by simultaneous ligase reaction with adapters blends for UC1, UC2, and UC3 so that the total adapter concentration for a given adapter is 40 nM. Reactions were carried out for 1 hour at room temperature in the presence of 0.8 U / ul of T4 DNA ligase. Particles were washed in TE buffer and scanned using Guava 6HT.

Example  14: Scanning multi-developed particles using commercial cell analyzers

In this example, general purpose particles prepared in Example 12 were used for scanning with commercial cell analyzers. Milipore Guave easyCyte 6HT-2L can be used as an exemplary cytometer for scanning.

Here, the particles were scanned with a cytometer using RED fluorescence for triggering phenomena, yellow fluorescence for code particle coding, and green fluorescence for particle orientation. As discussed, the particles shown in FIG. 27 consist of three active regions (barcode 1, probe and barcode 2) divided by two inactive regions. All three active regions have Cy5-modified nucleic acids and trigger phenomena in the Guava easyCyte cytometer RED2 channel. The Cy5 level of the probe region is intentionally made to be about half of the barcoded regions. Two barcoded regions have variable levels of Cy3-modified oligonucleotides. Cy3 levels of each barcoded region detected in the Guava cytometer YEL channel are used to give the particle a unique coding marker. In addition, higher levels of FAM6-modified oligonucleotides in barcode 1 are included in barcoded regions to provide an alignment means. A mixture containing 25 different particle barcodes with 5 unique Cy3 fluorescence levels at barcode 1 and 5 unique levels at barcode 2 was used for technical validation.

The threshold 500 set on the RED2 channel of Guava 6HT was sufficient to identify all three particle regions. Hundreds of particles at a concentration of about 20 per microliter in TE buffer were scanned at 0.6 microliters per second. The phenomena associated with particles plotted with YEL (barcoded color) vs. RED2 (triggered color) are shown in FIG. 29 with YEL vs. GRN (orientation). The particle probe area is shown in the lower left of the chart with lower levels of green (FAM-6 ™) and yellow (Cy3 ™). Two particle coding regions are shown in the upper right of the chart. A total of 10 bands are divided in the plot with 5 codes in the particle barcode 1 region and 5 codes in the barcode 2 region. Raw values appearing in these applications are sent to the FCS file for later analysis. All symptoms sent to CSV are stored in chronological order.

The phenomena sent from Guava software were analyzed and reconstructed using custom software based on RED2 and GRN fluorescence patterns. The software looks at the sequence of phenomena and evaluates whether these sequence phenomena match the expected patterns for RED2 and GRN fluorescence. If the pattern is correct, the phenomena are classified as particles and analyzed for barcodes in YEL fluorescence and oriented according to GRN fluorescence. After reconstruction, a more coherent plot is constructed using yellow intensity (Cy3 ™) levels in bar code 1 versus bar code 2 (design code 1 and code 2, respectively). This diagram is shown in FIG. Ellipses are used to identify particle clusters associated with each of the 25 barcodes present. It can be seen that the five levels of fluorescent barcode 1 (code 1) and barcode 2 (code 2) can be easily distinguished.

In addition to barcode determination, the on-demand software can also quantify the fluorescence associated with the capture target in the particle probe area, and this information is stored as the second of three phenomena associated with the particle. When using reporting phosphors that can be detected in the YEL channel, the YEL fluorescence level in this region indicates the target content present.

Example  15: single-vessel One - spot Development of isothermal nucleic acid amplification assay

This example shows the use of the encoded particles according to the invention in a variety of uses, for example nucleic acid amplification assays. As shown previously, Applicants have provided a variety of compositions that provide (1) sub-atomol sensitivity, (2) single-nucleotide specificity, (3) rapid scanning, (4) visible unlimited coding density, and (5) low cost And methods were developed. For example, the above examples, and in FIG. 31 show high performance analysis of microRNA targets. The simplicity, single-vessel analysis, and single-color detection of the present particle synthesis described herein allow for a new class of low cost diagnostic means.

In this project, we use coded hydrogel particle analysis to (1) perform accurate panel-based tests on DNA or RNA of> 10 pathogens at a time, (2) apply a quick and easy to use single-container, isothermal assay, and (3) We developed a point-of-care system using low-cost disposable cartridges in portable instruments. Applicants have employed a single-user (sample loading) single-vessel assay that can amplify specific genomic targets of pathogens, hybridize amplification products with barcoded gel particles, and quantify bound amplification products in a single sealed tube. Developing. Many species-specific targets are amplified with isothermal helicase-dependent amplification (HDA). The fluorescently-labeled amplification product diffuses into the encoded hydrogel particles and hybridizes with complementary nucleic acid probes embedded everywhere ( FIG. 32 ). The flexibility of this innovative micromachining process allows the pore size or particles to be tuned to exclude helicase enzymes (˜4.5 nm), thus releasing bound targets. With this advantage, the entire process can be performed without user intervention. After <1 hour, the particles are quickly scanned in the fluid channel using fluorescence to read each particle barcode and quantify the corresponding targets. It is an object to produce a cartridge-based system having disposable units in combination with a portable assay unit.

Applicants have also developed single-vessel assays using standard PCR described in the various examples above, and have recently studied isothermal assays according to the project objectives. L-phage DNA was used as a model system for assay development. First, Tm-matched primers for the two target regions of lambda were designed while controlling for human genomic DNA to avoid non-specific amplification. An amplification product of ~ 60bp length was designed. Probes were designed to target each amplification product with complementary sequences except for the binding site for the forward primer. Single-containers were performed with standard PCR and isothermal amplification ( FIG. 33 ).

For each assay, containing a single primer set (forward primer labeled Cy3), ˜50 encoded gel particles with two spatially-spaced probe regions for the amplification product, and lambda-phage DNA or human genomic DNA PCR mixes were prepared. Using both standard PCR and isothermal amplification, specific amplification and hybridization could be shown for each amplification product produced and no non-specific amplification of human genomic DNA. A series of dilutions were performed for lambda-phage at 11,000 to 11 copies per reaction. Using primer set # 1, it was possible to detect ˜11 copies of the template in this preliminary study by standard PCR using single-container assay. Sensitivity to isothermal reactions was not evaluated, but the signals observed for particles after 60-minute reactions were stronger signals than those obtained from standard PCR after 40 cycles.

Amplification Primers  And DNA  Detection probes design

For any pathogen, there is a need to identify genomic targets that are pathogen specific and conservative to modification. It is based on the development of others' PCR-based assays for four pathogens of interest. Targets for genomic HIV RNA: pol -integrase region and env and gag genes. PCR-based identifying targets for the typhoid genome include tyv, flag, viaB, and ratA genes. Conservation regions for the malaria protozoa genome include the 18s rRNA gene and the spore body (CS) gene. For dengue virus, Gurukumar et al. Targeted the conserved region in the 3'UTR of the conserved viral genome. First, the experiments are designed to target similar regions for these pathogens.

For multiplexed isothermal amplification, (1) design compatible primer sets that have similar melting points, (2) do not form hetero-dimers, and (3) specifically and efficiently amplify identified targets for each pathogen species. Needs to be. Since the particles are developing a "single-vessel" analysis present in the amplification reaction, (1) avoid the 3'-extension of the DNA probes embedded in the particle probe-regions, and (2) the present particles to which the amplification product hybridizes. It is necessary to consider maintaining a small amount (<100 kbp) so as to spread rapidly. To approach this approach, we will study a significant amount of books for primer design in multiplex amplification.

As shown in FIG. 34, primers will be designed to provide amplification products with melting points of approximately 55 ^° C., 20 bp in length, and 60 bp in size. For fluorescence detection the forward primers will have a single Cy3 label. For each pathogen species, several sets of primers will be designed that meet the above requirements. Primer design is achieved as follows:

First, a set of potential primers for co-targeting, conserved genomic regions for species of interest (dengue, typhoid, malaria, and HIV as well as l-phage and MS2 controls) using a primer-design program such as primer 3 Will be confirmed.

Second, each potential primer identified will be assessed for species-specificity via BLAST search.

Third, assess dimer-formation with all other primers (using nearest neighbor calculations) and total 30 primer sets (5 for each of 4 pathogens and 2 controls) that meet all requirements We will write a script in MATLAB to identify.

DNA  For detection Helicase -Dependent amplification ( HDA ) optimization.

In order to maximize the likelihood of success in developing potential isothermal amplification technology, we will start with commercially available kits and standard protocols that use lambda-phage as a model system. The model system will use the IsoAmp® kit (New England Biosciences), which can perform isothermal amplification on λ-phage ˜5000 copies added to human genomic DNA. Several, including (1) primer concentrations (0.1 uM-10 uM), (2) primer length (20-26 bp), (3) amplification temperature (50-65 C), and (4) reaction time (10-120 min) We will optimize the parameters. The efficiency and yield of the isothermal reaction will be assessed and compared with the yield of a standard 30-cycle PCR reaction using the same primers and target regions. Polyacrylamide gel electrophoresis (PAGE) will be used for this qualitative comparison using target band intensities as standardization criteria.

After optimization of the reaction conditions, the other species DNA primer set for (P. arm Shifa room, S., and Tai P) will now be examined the efficiency and specificity. Again, the target content generated in 10, 30, and 90 minute isothermal amplification will be quantified (via PAGE) to assess the amplification efficiency for each primer set. Specificity will be assessed by performing PCR with a primer set for a given species using human genomic DNA with ~ 5000 copies of the genomes for all other species added. Certain powerful reactions will only show amplification of the target sequence. Of the 5 primer sets designed for each species, we will use the 3 most efficient sets that show good specificity.

Three primer sets for each species will be used in the multiplex amplification assay where one target is present at a time. For multiplexing reactions, target amplification will be performed using the fluorescent forward primer shown in FIG. 34. For each reaction, the amplification product will be quantified by 30 min incubation with barcoded gel particles (FIG. 35) with probes for each amplification product. DNA probes for each particle will be designed to span the reverse primer and the inner region and will be capped at 3 'to avoid extension as shown in FIG. 35. This design allows for single-vessel amplification / capture in the following studies.

Ideally, the fluorescence signals observed in the particles would be consistent across the 3 amplification products generated for each species. If a significant difference in amplification / capture efficiency is observed for multiplexed amplification, several reaction conditions will be altered to normalize the trapped amplification product content in each particle probe region. First, the relative contents of the primers are adjusted to change the reaction kinetics accordingly. Second, the primer length is adjusted to change the binding efficiency-this affects primer Tm and increases nonspecific amplification, which would therefore be undesirable. Third, it was shown that the binding rate could be adjusted in a predictable manner by changing the probe concentration in each region of the particles.

After normalizing the quantification signal for each species, a single-vessel analysis will be performed in which amplification and hybridization are completed in the same reaction. The effect of particles on sensitivity and primer sets specificity will be determined. Repeated optimization of primer and probe sequences will be required along with reaction temperature and cycle. In the case of multiplexing, single-vessel analyzes, particles will be imaged in static (microscopic) and fluid flow modes. The sensitivity and reproducibility of the two methods will be monitored and compared-these are important considerations when designing the integral system proposed in Example 17.

Of pathogen dielectric material Reverse transcription .

P. Shifa arm room and S. tie direct amplification of blood genomic DNA, but both the RNA genome is reverse transcribed to detect amplification and analysis for cDNA for HIV-1 and dengue viruses, which are ssRNA virus is required. It is necessary to add reverse transcriptase to the isothermal amplification reaction. Reverse transcription has been successfully combined with helicase-dependent amplification and isothermal RT-HAD kits are commercially available (IsoAmp®, NE Biolabs). This is the same kit used in the previous studies.

We will begin with standard recommendation protocols for RNA reverse transcription and cDNA amplification using phage MS2 as a model system for optimization. Similar optimizations will be performed as performed for DNA amplification, using the 5 primer sets originally identified for phage MS2. Once optimized, primer sets for pathogen RNA targets, again quantification amplification efficiency and specificity will be assessed. Using the three best primer sets for each RNA species, multiple amplifications will be performed for each. Again, coded gel particles will be used to quantify amplification products in static and fluid flow modes.

Pathogen DNA or RNA  Single-vessel analysis optimization for multiplexed detection.

Multiple detections of both DNA targets and RNA targets will be independently optimized and these assays will be combined to optimize performance and speed. Using the human genomic DNA background, samples will be added to each sample at concentrations ranging from 1-100,000 copies. Primer concentrations, enzyme concentrations, assay duration, and assay temperature will be examined and optimized. Specificity, detection limit, and sensitivity at 100 copies / rxn will be measured to assess assay performance for each pathogen. The goal is to show 95% sensitivity for all pathogens at 100 copies / rxn with 60 min analysis time.

Although it is ideal to use isothermal amplification with a single-step amplification / hybridization reaction that can detect both DNA and RNA species in a single sample, there are several alternative approaches that are less attractive but more successful.

For example, if helicase-dependent amplification (HDA) is not effective, including loop-mediated isothermal amplification (LAMP), strand-replacement amplification (SDA), and nucleic acid sequence-based amplification (NASBA) Several other isothermal methods will be studied. Importantly, NASBA-based assays have already been approved by the FDA for HIV-1 detection and thus may be an obvious next choice for RNA detection. Alternatively, standard PCR can be used. Indeed, microfluidic methods for PCR amplification are so common that it may not be possible to use this approach. In addition, if detecting RNA pathogens and DNA pathogens (requires reverse transcription) in the same tube poses a difficult problem to solve, these assays can be divided into two separate tests.

In some embodiments, as an alternative to single-vessel assays, two-step amplification / hybridization can be used in accordance with the present invention. If the particles interfere with the amplification process in any way, it may be necessary to perform the amplification and hybridization separately. Imagine a cartridge-based system in which this method can be implemented, the assay can still be achieved on-chip but will require some more sophisticated liquid handling. This is not an ideal situation, but it is affordable and actually meets the diagnostic need in developing countries.

Example  16. Detection of Multiplexed Pathogens For single -Containment analysis verification

After developing a single-vessel assay for detecting multiple pathogens in Example 15, we validated this using clinically-relevant samples and developed a pathogen-specific assay for quantitative PCR, which is currently the optimal standard for nucleic acid-based pathogen diagnosis. Will be compared. This objective will be important in demonstrating the clinical utility of this assay.

Representative clinical-related sample sets will be obtained from several partners. Without being bound by any particular theory, the samples obtained will be well-preserved. This is especially important for RNA detection because RNA degrades quickly due to RNase activity. If sufficient samples are available, quality control through DNA / RNA sizing will be performed with the Agilent Bioanalyzer. Another assumption is that these samples are representative samples that can be obtained in the field of the present technology. Ideally, the samples cover a wide range of pathogen loads and patient immune response status.

There are several steps to verify this analysis. First, various methods of purifying nucleic acids from whole blood will be studied and the suitability of this assay for each pathogen will be determined. This will be important in determining which purification technologies will be integrated with the platform after this initial research project is completed. Ideally we would choose one isolation technique that performed well for all pathogens and use it for all validation tests. Nucleic acids will be purified from clinical samples (blood or plasma) provided by the collaborators and the samples will be tested using this single-container test and commercially available pathogen qPCR kits. This allows a direct comparison of this analysis to the current state of the art in the field. Details of each part of the verification process are given below.

Evaluation of Nucleic Acid Purification Technology . There are several ways to extract nucleic acids from whole blood, plasma, or serum. Most kits are specific for RNA or DNA, and some kits are used to extract both. We will examine several commercially available kits, including:

DNA extraction: QIAamp Blood DNA Mini Extraction Kit (QIAGEN), Genomic DNA Extraction Kit (Bioneer), Extract-N-Amp Blood PCR Kits (Sigma).

RNA extraction: QIAmp Viral RNA Mini Extraction Kit (QIAGEN), Viral RNA Extraction Kit (Bioneer).

Simultaneous DNA and RNA extraction: QIAamp MinElute Virus Spin Kit, QIAamp UltraSens Virus Kit, NucleoSpin Virus Kit (Macherey-Na gel).

Clearly, the optimal mode for multiplexing analysis is to use a single extraction method for parallel separation of pathogen DNA and RNA. Considerable efforts will be made in identifying and optimizing methods for this single-container assay and well-functioning double nucleic acid extraction. For conformity assessment, well-characterized clinical samples containing each pathogen will be extracted into the respective kits. Samples will then be evaluated with this single-vessel assay and also validated using qPCR kits specifically designed for each pathogen.

Analysis of clinical samples compared directly with qPCR . Nucleic acids from clinical samples (at least 30 for each pathogen type) will be purified by the optimal method determined in the section above. A single-container, multiplexed assay for the detection of pathogens in each sample will be performed and the results will be compared with qPCR assays designed specifically for each pathogen. For three of the four test pathogens, there are several qPCR kits available. When this goal is reached, a kit that performs optimally is selected and certified for diagnostic testing:

Dengue: Primer Design, Ltd. And Genome Diagnostics

Malaria: Primer Design, Ltd., AccuPower, and Genome Diagnostics

HIV- 1: Primer Design, Ltd. And Genome Diagnostics

Typhoid fever: in the category known, commercially tie against S. P-qPCR analysis is not available. There is a multiplexed PCR-based approach by Kumar et al. That can be used as an alternative to qPCR if tests are not developed until the project objectives are reached.

For relative comparison of sensitivity, a series of dilutions will be performed on representative samples for each pathogen type and analyzed using this assay and qPCR standards. Strong correlation between the results of this analysis and the current state of the art is important in the verification. If this assay is performed less desirably than expected, the target areas, primer designs, and assay conditions will be re-evaluated to solve the assay problem. We will work confidentially with our partners to solve any problems.

Example  17: Development of integrated system technology verification

After successfully developing the assay, it is important to start conceptualizing the analytical methods implemented on the chip. For this reason, a method will be developed for performing single-vessel analysis and for analyzing particles in a single chamber. This requires the development of an integrated system capable of precise temperature control with fast signal acquisition for fluorescence imaging or fluid flow analysis for static particle analysis. The system allows periodic analysis of the particles to assess the reaction situation. As a significant improvement over endpoint analysis, it has been shown that calibration of this assay can provide precise quantitative analysis of pathogen load. In this example, the goal is to develop an integrated system for performing rapid, single-vessel analyzes that can accurately quantify pathogen nucleic acids.

As the simplest initial method, one would use a commercially-available temperature-controlled cell perfusion chamber that can be statically imaged under a microscope. Further studies will be conducted to evaluate the use of single-chamber chamber reactions for pathogen detection and to evaluate the feasibility of quantitative analysis with periodic image analysis. After successful implementation, the heating flow chamber will be integrated into a stand-alone device with an LED light source and a CCD camera for image acquisition. This is an important step in the development of cartridge-based systems that will ultimately be deployed in developing countries. Details of the specific activities for this purpose are given below.

Single -vessel analyzes in a heated flow cell . Commercially-available heated flow cells similar to those sold by Bioptechs will be used. These flow cells feature (1) custom channel design, (2) multiple interfaces for sample introduction, (3) precision temperature control with +/- 0.2 ^o C stability, and (4) any microscope It's a standard design. Initially, a simple rectangular flow chamber will be utilized for identification and analysis. The reaction mixture comprising ˜50 particles for the sample of interest, isothermal amplification reagents, and 4 pathogens and 2 controls, respectively, will be premixed. The instrument will be preheated to an isothermal amplification temperature (˜55 ^o C) and the reaction mixture will be introduced into the reaction chamber. A standard inverted microscope with a 5 × objective (for a wide field of view), a single excitation color, and a single detection color will be used to image the particles during the amplification process, eg every 5 minutes. Each image will be analyzed and an estimate of each amplification product generated based on probe-area fluorescence. After a 60 minute reaction, this dynamic data will be used to estimate the initial content of template present. For technical validation, 2 controls, lambda-phage DNA and phage MS2 will be used to characterize system performance and ability to provide quantitative data.

Integrated Analysis / Scanning System Design and Fabrication . After the microscope-based system has been successfully implemented, the flow cell will be integrated into the custom optical system. Uniform LED lighting, low-magnification lenses, and CCD chips will be utilized. An LED array, CCD, and heated flow cell will be connected to the laptop computer for control, image acquisition, and analysis. We will fully test this unit and compare the results with those already obtained in this project. The device will be used to reevaluate the sensitivity and specificity of each pathogen detection. We will also add targets of 1-1M copies to review the quantitative dynamic range of the system. Measures will be taken to ensure that performance is working properly in the integrated system.

All documents and similar materials cited herein, including patents, patent applications, articles, books, thesis, university thesis and web pages, are hereby expressly incorporated by reference in their entirety, regardless of the form of documents and similar materials. do. In the event that one or more of the documents and similar materials included above, including defined terms, term usage, described techniques, or the like, differ from or contradict this application, the present application controls.

The section headings used herein are for specification purposes only and should not be construed as limiting the subject matter in any way.

Etc Examples  And equality theory

Although the present invention has been described in connection with various embodiments and embodiments, it is not limited to these embodiments or embodiments. On the contrary, the invention encompasses various alternatives, modifications, and equivalents, as will be appreciated by those skilled in the art. Accordingly, the descriptions, methods, and drawings are not to be limitedly read in a written order unless explicitly stated.

While the present invention has been described and illustrated with certain embodiments, it is to be understood that the invention is not limited to these specific embodiments. Rather, the invention is to cover all embodiments that are functional and / or equivalent of the specific embodiments and features described and illustrated.

The claims are as follows:

                         SEQUENCE LISTING <110> Firefly Bioworks, Inc.   <120> Nucleic Acid Detection and Quantificatioin by Post-Hybridization        Labeling and Universal Encoding <130> 2009677-0004 <150> US 61/352018 <151> 2010-06-07 <150> US 61/365738 <151> 2010-07-19 <150> US 61/387958 <151> 2010-09-29 <160> 45 <170> PatentIn version 3.5 <210> 1 <211> 34 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for let-7a <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature (222) (34) .. (34) <223> 3 'inverted dT <400> 1 gatatatttt aaactataca acctactacc tcat 34 <210> 2 <211> 34 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-21 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature (222) (34) .. (34) <223> 3 'inverted dT <400> 2 gatatatttt atcaacatca gtctgataag ctat 34 <210> 3 <211> 35 <212> DNA <213> Artificial Sequence <220> <223> probe sequence fof miR-29b-2 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 > (35) <223> 3 'inverted dT <400> 3 gatatatttt aaacactgat ttcaaatggt gctat 35 <210> 4 <211> 35 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-18ab-1 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 > (35) <223> 3 'inverted dT <400> 4 gatatatttt aacccaccga cagcaatgaa tgttt 35 <210> 5 <211> 33 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-143 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 > (33) <223> 3 'inverted dT <400> 5 gatatatttt agagctacag tgcttcatct cat 33 <210> 6 <211> 35 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-145 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 > (35) <223> 3 'inverted dT <400> 6 gatatatttt aagggattcc tgggaaaact ggact 35 <210> 7 <211> 34 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-146a <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature (222) (34) .. (34) <223> 3 'inverted dT <400> 7 gatatatttt aaacccatgg aattcagttc tcat 34 <210> 8 <211> 34 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-210 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature (222) (34) .. (34) <223> 3 'inverted dT <400> 8 gatatatttt atcagccgct gtcacacgca cagt 34 <210> 9 <211> 35 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-221 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 &gt; (35) <223> 3 'inverted dT <400> 9 gatatatttt agaaacccag cagacaatgt agctt 35 <210> 10 <211> 33 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miR-222 <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 &gt; (33) <223> 3 'inverted dT <400> 10 gatatatttt aacccagtag ccagatgtag ctt 33 <210> 11 <211> 33 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for miSpike <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 &gt; (33) <223> 3 'inverted dT <400> 11 gatatatttt aagaccgctc cgccatcctg agt 33 <210> 12 <211> 54 <212> DNA <213> Artificial Sequence <220> <223> probe sequence for RNU6B <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature &Lt; 222 &gt; (54) <223> 3 'inverted dT <400> 12 gatatatttt aaaaaatatg gaacgcttca cgaatttgcg tgtcatcctt gcgt 54 <210> 13 <211> 34 <212> DNA <213> Artificial Sequence <220> <223> let-7a probe <220> <221> misc_feature <222> (1) <223> 5 'acrydite <220> <221> misc_feature (222) (34) .. (34) <223> 3 'inverted dT <400> 13 gatatatttt aaactataca acctactacc tcat 34 <210> 14 <211> 22 <212> RNA <213> Artificial Sequence <220> <223> let-7a target <400> 14 ugagguagua gguuguauag uu 22 <210> 15 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UA10-Cy3 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'Cy3 <400> 15 taaaatatat 10 <210> 16 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UA10-bio <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'biotin <400> 16 taaaatatat 10 <210> 17 <211> 13 <212> DNA <213> Artificial Sequence <220> <223> UA10-bio <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (13) <223> 3 'biotin <400> 17 taaaatatat aaa 13 <210> 18 <211> 16 <212> DNA <213> Artificial Sequence <220> <223> UA10-bio <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (16) <223> 3 'biotin <400> 18 taaaatatat aaaaaa 16 <210> 19 <211> 22 <212> DNA <213> Artificial Sequence <220> <223> UA10-bio <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (22) <223> 3 'biotin <400> 19 taaaatatat aaaaaaaaaa aa 22 <210> 20 <211> 21 <212> RNA <213> Artificial Sequence <220> <223> Sequences for mature miR-143 <400> 20 ugagaugaag cacuguagcu c 21 <210> 21 <211> 55 <212> RNA <213> Artificial Sequence <220> <223> Sequences for precursor miR-143 <400> 21 ggugcagugc ugcaucucug gucaguuggg agucugagau gaagcacugu agcuc 55 <210> 22 <211> 32 <212> DNA <213> Artificial Sequence <220> <223> probe for labeling the 3 'end of mature miR-143 <220> <221> misc_feature <222> (1) <223> 5 'acrylate <400> 22 gatatatttt agagctacag tgcttcatct ca 32 <210> 23 <211> 31 <212> DNA <213> Artificial Sequence <220> <223> probe for labeling the 5 'end of mature miR-143 <220> <221> misc_feature <222> (1) <223> 5 'acrylate <400> 23 gagctacagt gcttcatctc aatttatatt t 31 <210> 24 <211> 22 <212> DNA <213> Artificial Sequence <220> <223> adapter sequence for 3 'labeling <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (22) <223> 3 'biotin <400> 24 taaaatatat aaaaaaaaaa aa 22 <210> 25 <211> 15 <212> RNA <213> Artificial Sequence <220> <223> adapter sequence for 5 'labeling <220> <221> misc_feature <222> (1) <223> 5 'biotin <400> 25 aaaaaaaaau auaau 15 <210> 26 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> stem-loop encoding probe <220> <221> misc_feature <222> (1) <223> 5 'acrydite <400> 26 aataaacacg ggaataaccc 20 <210> 27 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> probe anchor <220> <221> misc_feature <222> (1) <223> 5 'acrydite <400> 27 gatatatttt 10 <210> 28 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> fluorescently-labeled encoding adapter <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> Cy3 <400> 28 gtgtttataa 10 <210> 29 <211> 11 <212> DNA <213> Artificial Sequence <220> <223> unlabeled adapter <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (11) <223> inverted dT <400> 29 gtgtttataa t 11 <210> 30 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> UCode1 probe <220> <221> misc_feature <222> (1) <223> 5 'acrydite <400> 30 aataaacacg ggaataaccc 20 <210> 31 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> UCode2 probe <220> <221> misc_feature <222> (1) <223> 5 'acrydite <400> 31 aataatgtgc ccaataaggg 20 <210> 32 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UCode 1 adapter Cy3 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature (222) (9) .. (9) <223> 3 'Cy3Sp <400> 32 gtgtttatta 10 <210> 33 <211> 11 <212> DNA <213> Artificial Sequence <220> <223> UCode 1 adapter invdT <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (11) <223> 3 'inverted dT <400> 33 gtgtttatta t 11 <210> 34 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UCode 2 adapter Cy3 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'Cy3Sp <400> 34 cacattatta 10 <210> 35 <211> 11 <212> DNA <213> Artificial Sequence <220> <223> UCode 2 adapter invdT <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (11) <223> 3 'inverted dT <400> 35 cacattatta t 11 <210> 36 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> UC1 <220> <221> misc_feature <222> (1) <223> 5 'acrylate <400> 36 aataaacacg ggaataaccc 20 <210> 37 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> US2 <220> <221> misc_feature <222> (1) <223> 5 'acrylate <400> 37 aataatgtgc ccaataaggg 20 <210> 38 <211> 20 <212> DNA <213> Artificial Sequence <220> <223> UC3 <220> <221> misc_feature <222> (1) <223> 5 'acrylate <400> 38 aataactctg ggaataaccc 20 <210> 39 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC1-A-Cy3 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'Cy3 <400> 39 gtgtttatta 10 <210> 40 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC1-A-NF <220> <221> misc_feature <222> (1) <223> 5 'phosphate <400> 40 gtgtttatta 10 <210> 41 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC1-A-FAM6 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'FAM6 <400> 41 gtgtttatta 10 <210> 42 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC2-Cy5 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'Cy5 <400> 42 cacattatta 10 <210> 43 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC3-A-Cy3 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'Cy3 <400> 43 agagttatta 10 <210> 44 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC3-A-NF <220> <221> misc_feature <222> (1) <223> 5 'phosphate <400> 44 agagttatta 10 <210> 45 <211> 10 <212> DNA <213> Artificial Sequence <220> <223> UC3-A-FAM6 <220> <221> misc_feature <222> (1) <223> 5 'phosphate <220> <221> misc_feature &Lt; 222 &gt; (10) <223> 3 'FAM6 <400> 45 agagttatta 10

Claims (129)

A nucleic acid probe comprising at least one region having one or more nucleic acid probes, wherein each nucleic acid probe binds to the target nucleic acid such that binding of both the target nucleic acid and the universal adapter to the same nucleic acid probe is detectable by post-hybrid labeling; A substrate, consisting of contiguous adapter sequences that bind a universal adapter. The substrate of claim 1, wherein the binding sequence and the adapter sequence are configured such that when the target nucleic acid and the universal adapter are bound to the same nucleic acid probe, the target nucleic acid is linked with the universal adapter. The substrate of claim 2, wherein when both the target nucleic acid and the universal adapter are bound to the same nucleic acid probe, the capture sequence and the adapter sequence are configured such that the target nucleic acid is linked to the universal adapter by an enzyme or chemical bond. 4. The substrate of claim 2, wherein the capture sequence and adapter sequence are constructed such that when both the target nucleic acid and the universal adapter are bound to the same nucleic acid probe, the target nucleic acid is linked to the universal adapter by DNA or RNA ligase. The substrate of claim 1, wherein the adapter sequence is designed to minimize secondary structure of the probe. The substrate of claim 1, wherein the capture sequence and the adapter sequence are designed such that the capture sequence melting point is higher than the adapter sequence melting point. The substrate of any one of the preceding claims, wherein the probe comprises a capped 3 'end to inhibit ligase reaction. The substrate of claim 1, wherein the substrate has a planar, spherical or non-spherical surface. The substrate of claim 8, wherein the substrate is microarray. The substrate of claim 8, wherein the substrate is a particle. The substrate of claim 10, wherein the particles are glass, polymer, hydrogel, silica, or metal. The substrate of claim 11, wherein the particles are hydrogels. The substrate of claim 10, wherein the particle comprises one or more coding regions. The substrate of claim 13, wherein the one or more coding regions are graphically and / or fluorescently encoded. The substrate of claim 13, wherein the one or more coding regions are spaced from the at least one probe region by inactive regions. The substrate of claim 13 or 14, wherein the one or more coding regions overlap with at least one probe region. The substrate of claim 1, wherein the particle has a signal indicating particle orientation. A nucleic acid probe comprising a capture sequence that binds a target nucleic acid and a contiguous adapter sequence that binds a universal adapter such that the binding of both the target nucleic acid and the universal adapter to the nucleic acid probe is detectable by post-hybrid labeling. The nucleic acid probe of claim 18, further comprising a nucleic acid barcode sequence that captures the nucleic acid probe at a specific position. The nucleic acid probe according to claim 18 or 19, further comprising a moiety that enzymatically or chemically connects the nucleic acid probe to the substrate surface. The nucleic acid probe of claim 18, wherein the nucleic acid probe is single-stranded DNA. The nucleic acid probe of claim 18, wherein the capture sequence is designed complementary to the 3 ′ terminal sequence of the microRNA of interest. A substrate comprising one or more universal coding regions, each universal coding region having one or more single-stranded polynucleotide templates, each template consisting of a stem-loop structure and a predetermined nucleotide sequence adjacent to the stem-loop structure. The substrate of claim 23, wherein the predetermined nucleotide sequence is a predetermined 10-base sequence. The substrate of claim 23, wherein the predetermined nucleotide sequence has a 4-nucleotide sequence unique to only a 6-nucleotide sequence and a subset common to all predetermined sequences. The substrate of claim 23, wherein the particle further comprises one or more general purpose probe regions. 27. The substrate of claim 26, wherein each general purpose probe region has one or more anchors for attaching probes of interest to the particle. The substrate of claim 27, wherein the one or more anchors are nucleic acid anchors. The substrate of claim 28, wherein the individual nucleic acid anchors consist of a hairpin structure. The substrate of claim 29, wherein the individual nucleic acid anchors have a linear structure. The substrate of claim 27, wherein the one or more anchors are chemical anchors. The substrate of claim 31, wherein the one or more anchors comprise one or more carboxyl groups, amine groups, thiol groups, and / or azide groups. 33. The substrate of any one of claims 23 to 32, wherein the one or more universal coding regions are spaced apart from the one or more universal probe regions by inactive regions. 33. The substrate of any one of claims 23-32, wherein the one or more general purpose coding regions overlap with the one or more general purpose probe regions. 25. The substrate of any one of claims 16 to 24, wherein the particle further comprises one or more encoding adapters attached to one or more polynucleotide templates. The substrate of claim 25, wherein the individual encoding adapters comprise a nucleotide sequence complementary to a predetermined nucleotide sequence of the polynucleotide template of interest. The substrate of claim 35 or 36, wherein the individual encoded adapters consist of up to 30 nucleotides. 38. The substrate of any one of claims 35 to 37, wherein the one or more encoded adapters consists of a combination of labeled and unlabeled encoded adapters. The substrate of claim 38, wherein the labeled encoding adapters are comprised of a detectable substance. The substrate of claim 39, wherein the detectable substance is a phosphor, chromophore, radioisotope, quantum dots, nanoparticles and / or insert DNA / RNA dyes. 41. The substrate of any one of claims 38-40, wherein the labeled encoding adapters are labeled with a distinct detectable substance. 42. The substrate of any one of claims 38-41, wherein there are labeled and unlabeled encoded adapters in a ratio at which a desired detectable signal level is achieved in each encoded region. 42. The substrate of any one of claims 38-41, wherein at least one label encoding adapter is present at a level suitable for signal normalization for other label encoding adapters. 43. The substrate of any one of claims 38-42, wherein at least one label encoding adapter is present at a level suitable for indicating particle orientation. 45. The substrate of any one of claims 27-44, wherein the particle further comprises one or more probes of interest that are attached to one or more anchors in the universal probe regions. 46. The substrate of claim 45, wherein the one or more probes of interest are directly attached to one or more anchors. 46. The substrate of claim 45, wherein the one or more probes of interest are attached to one or more anchors via a linker. 48. The substrate of any one of claims 45-47, wherein the one or more probes are designed to detect a plurality of target nucleic acids of interest. a. Contacting a sample with a plurality of nucleic acid probes each consisting of a capture sequence that binds a target nucleic acid and a contiguous adapter sequence that binds a universal adapter;
b. Culturing the plurality of probes and the sample under conditions in which one or more universal adapters are present and both individual target nucleic acids and individual universal adapters can be bound to the same individual nucleic acid probe;
c. Conducting the reaction so that the individual universal adapters are combined with the individual target nucleic acids, and hybridizing with the same individual nucleic acid probe;
d. Detecting the presence and / or abundance of target nucleic acids in the sample, including detecting the presence of one or more general purpose adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of target nucleic acids in the sample. How to. The method of claim 49, wherein the plurality of nucleic acid probes are attached to a substrate. The method of claim 49, wherein each nucleic acid probe further comprises a barcode sequence that captures the nucleic acid probe at a substrate specific location. 52. The method of claim 50 or 51, wherein the substrate is microarray. The method of claim 50 or 51, wherein the substrate is a particle. The presence of target nucleic acids in a sample of any one of claims 49-53, wherein the condition in step (b) causes the individual target nucleic acids and the individual universal adapters to bind to the same individual nucleic acid probe at the same time. And / or a method of detecting water. 55. The method of any one of claims 49-53, wherein the condition in step (b) is such that the presence of the target nucleic acids in the sample, such that the individual target nucleic acid and the individual universal adapters are sequentially coupled to the same individual nucleic acid probe, and And / or a method of detecting water. 56. The method of any one of claims 49-55, wherein the method further comprises removing unbound universal adapters after the binding step. 54. The method of any one of claims 49-53, wherein the method further comprises removing unbound universal target nucleic acids after the binding step. . The method of any one of claims 49-56, wherein the one or more general purpose adapters are labeled by one or more detectable substances. 59. The method of any one of claims 49-58, wherein each one or more detectable substances are from the group consisting of phosphors, chromophores, radioisotopes, quantum dots, nanoparticles, intercalating DNA / RNA dyes, and combinations thereof. Independently selected, the method for detecting the presence and / or number of target nucleic acids in a sample. 60. The method of claim 59, wherein the one or more detectable substances consist of phosphors. 57. The method of any one of claims 49-56, wherein at least one of the one or more universal adapters is biotinylated. 62. The method of claim 61, wherein the method comprises the steps of culturing the streptavidin reporter and subjects bound to phycoetrine, PE-Cy5, PE-Cy5.5, PE-Cy7, APC, PerCP, quantum dots, or phosphors. Further comprising, the presence and / or number of target nucleic acids in the sample. 62. The method of claim 61, wherein the method further comprises culturing the streptavidin reporter and subjects bound to the enzyme for generating an enzyme signal. 64. The method of claim 63, wherein the enzyme is alkaline phosphatase, beta-galactosidase, or mustard peroxidase. 65. The method according to claim 63 or 64, wherein the presence and / or number of target nucleic acids in the sample is capable of detecting chemiluminescence, fluorescence, or color development by enzyme signal generation. 66. The method of any one of claims 49-65, wherein the reaction in step c is an enzymatic binding reaction. 67. The method of claim 66, wherein the enzymatic binding reaction is a ligase reaction. The method of claim 67, wherein the ligase reaction detects the presence and / or number of target nucleic acids in the sample involving DNA ligase, RNA ligase, and / or polymerase. 69. The method of any one of claims 49-68, wherein each individual subject comprises one or more encoded regions indicative of the subject identification. The method of claim 69, wherein the one or more coding regions are graphically and / or fluorescently encoded. The method of any one of claims 49-70, wherein each individual subject has a signal indicative of subject orientation. 72. The method of any one of claims 49-71, wherein the detecting step comprises scanning a plurality of subjects with a fluid flow device. 73. The method of claim 72, wherein the fluid flow mechanism is a flow cytometer. The method of claim 72, wherein the scanning step is performed above the universal adapter melting point but below the bound target-adapter melting point. 75. The method of claim 74, wherein the method does not comprise the step of removing unbound universal adapters. 76. The method of any one of claims 49-75, wherein the method further comprises the step of quantifying the target nucleic acid content. The method of claim 76, wherein the quantifying step quantitatively determines the level of detectable signals associated with one or more general purpose adapters. 78. The method of any one of claims 49-77, wherein the target nucleic acids consist of DNA and / or RNA. 79. The method of claim 78, wherein the target nucleic acids are comprised of microRNAs. 80. The method of claim 79, wherein the microRNA is a mature microRNA. 81. The method of any one of claims 49-80, wherein the adapter sequence in the probe is at the 3 'end of the target capture sequence and detects the presence and / or number of target nucleic acids in the sample. 81. The method of any one of claims 49-80, wherein the adapter sequence in the probe is at the 5 'end of the target capture sequence. The presence of target nucleic acids in a sample according to claim 49, wherein the adapter sequence in the probe is positioned at the end of the target capture sequence in a manner that effectively labels the mature species and does not label the precursor species. And / or a method of detecting water. 84. The target of any one of claims 49-83, wherein the target nucleic acids consist of a plurality of nucleic acid species and the plurality of nucleic acid species have variable nucleotide sequences at one end and identical nucleotide sequences at the other end. A method for detecting the presence and / or number of nucleic acids. 85. The sample of claim 84, wherein the capture sequence adjacent to the adapter sequence in the nucleic acid probe indicates the presence of the desired terminal variable target nucleic acid in the sample by universal adapter detection designed complementary to the desired variable terminal nucleotide sequence and linked to the probe. A method for detecting the presence and / or number of target nucleic acids in a cell. 86. The method of any one of claims 49-85, wherein the target nucleic acids are present in the sample in low numbers. 87. The method of claim 86, wherein the target nucleic acids are present at a level of 0.1 amol-10,000 amol. The method of claim 86, wherein the target nucleic acids are present at levels up to 200 amol. The method of claim 86, wherein less than 1% of the total nucleic acids in the sample are target nucleic acids. The method of claim 86, wherein less than 0.1% of the total nucleic acids in the sample are target nucleic acids. 87. The method of claim 86, wherein less than one million total nucleic acids in the sample are target nucleic acids. 87. The method of claim 86, wherein less than one tenth of the total nucleic acids in the sample are target nucleic acids. 99. The sample of any of claims 49-92, wherein the sample comprises synthetic nucleic acids, purified RNA or DNA, reverse electron or amplified nucleic acids, cells, cell lysate, tissue, tissue lysate, whole blood, plasma, serum. Of target nucleic acids in a sample selected from the group consisting of urine, feces, saliva, umbilical cord blood, chorionic villus sample, chorionic villus sample culture, amniotic fluid, amniotic fluid, and cervical lavage fluid, and combinations thereof. A method of detecting presence and / or water. 94. The disease of any one of claims 49-93, wherein the sample is selected from tissue damage, acute myocardial infarction, asthma, heart disease, HCV infection, liver disease, arthritis, pulmonary disease, diabetes, Alzheimer's and / or cancer. A method for detecting the presence and / or number of target nucleic acids in a sample, taken from a patient suffering from or vulnerable thereto. 95. The method of any one of claims 49-94, wherein the subjects are particles. 97. The method of claim 95, wherein each particle is independently planar, spherical or non-spherical. 98. The method of claim 95 or 96, wherein each particle is independently selected from the group consisting of glass, polymer, hydrogel, silica, metal, and any combination thereof, and / or the presence and / or number of target nucleic acids in the sample. How to detect. a. A plurality of nucleic acid probes comprising a capture sequence that binds a target nucleic acid of interest and a contiguous adapter sequence that binds a universal adapter; And
b. A kit for detecting target nucleic acids, consisting of one or more universal adapters. 99. The kit of claim 98, wherein the plurality of nucleic acids are attached to a plurality of substrates. The kit for detecting target nucleic acids according to claim 98 or 99, further comprising one or more of the following components:
c. Hybridization reagents;
d. Universal adapters and reagents for binding to target nucleic acids; And
e. Wash buffer. 101. The kit of any of claims 98-100, wherein one or more general purpose adapters are labeled with one or more detectable substances. 101. The kit of any of claims 98-100, wherein at least one of the one or more universal adapters is biotinylated.  107. The kit of claim 102, further comprising a phycoetrine-binding streptavidin reporter. a. Providing a substrate comprising one or more coding regions, each having one or more single-stranded polynucleotide templates;
b. The labeled single-stranded coding adapter each comprising a sequence designed to specifically bind to an individual polynucleotide template, the labeling single-stranded coding adapter providing a plurality of labeled and unlabeled single-stranded coding adapters comprising a detectable substance;
c. Culturing the substrate and a plurality of labeled and unlabeled single-stranded adapters under conditions such that the individual encoded adapters can bind with the corresponding single-stranded polynucleotide template;
d. Binding the individual encoding adapters to the corresponding polynucleotide template, thereby encoding the substrate. 105. The method of claim 104, wherein the individual single-stranded polynucleotide templates form a hairpin structure and the individual single-stranded coding adapters do not form a hairpin structure. 107. The method of claim 104, wherein the individual single-stranded coding adapters form a hairpin structure and the individual single-stranded polynucleotide templates do not form a hairpin structure. 107. The method of any one of claims 104-106, wherein the plurality of labeled and unlabeled single-stranded coding adapters comprises a plurality of detectable substances. 107. The method of claim 107, wherein each of the plurality of detectable materials is independently selected from phosphors, chromophores, radioisotopes, quantum dots, nanoparticles, and / or insert DNA / RNA dyes. 107. The method of any one of claims 104-108, wherein the plurality of labeled and unlabeled single-stranded coded adapters consists of one or more sets of labeled and unlabeled coded adapters, in each set of labeled And the unlabeled encoding adapters have substantially identical sequences except for a detectable substance. 109. The method of claim 109, wherein the one or more sets are labeled with distinct detectable substances. 119. The method of claim 109 or 110, wherein each set of labeled and unlabeled adapters binds to the same individual polynucleotide template. 117. The method of any one of claims 109-111, wherein in each set, the labeled and unlabeled encoded adapters are present at a predetermined rate capable of achieving the desired signal level in each encoded region. 117. The method of any one of claims 104-112, wherein at least one label encoding adapter is used for normalizing detectable signals for other label encoding adapters. 117. The method of any one of claims 104-112, wherein the signal level of at least one label encoding adapter is used to determine substrate orientation. 117. The method of any one of claims 104-112, wherein one or more coding regions in the substrate are spaced apart by inactive regions. 116. The method of any one of claims 104-115, wherein the substrates and coding adapters are designed such that each coding region is labeled with a plurality of coding adapters. 117. The method of any one of claims 104-116, wherein the level of detectable signals provided by the encoding adapters in one or more encoding regions is used for substrate identification determination. 118. The method of any one of claims 104-117, wherein the substrate further comprises one or more probe regions, each probe region having one or more anchors for attaching the probes of interest to the substrate. 118. The method of claim 118, further comprising providing a plurality of probes of interest and attaching the probes to one or more anchors. 119. The method of claim 118 or 119, wherein the one or more anchors are nucleic acid anchors.  119. The method of claim 118 or 119, wherein the one or more anchors are chemical anchors. 121. The method of claim 121, wherein the one or more anchors comprise one or more carboxyl groups, amine groups, thiol groups, and / or azide groups. 124. The method of claim 104, wherein the substrate is selected from the group consisting of particles, beads, phages, macromolecules, cells, microorganisms, and combinations thereof. 123. The method of any one of claims 104-123, wherein the substrate is a particle. 124. The method of claim 124, wherein the particles are spherical or non-spherical. 126. The method of claim 124 or 125, wherein the particles are glass, polymer, hydrogel, silica, or metal. 129. The method of any one of claims 124-126, wherein the particles are hydrogel particles. 127. A substrate encoded using the method of any of claims 104-127. 127. Particles encoded using the method of any one of claims 104-127.

Images